Indonesian differs from the Malaysian language in a number of respects, primarily due to the different influences both languages experienced and also due to the fact that majority of Indonesians speaks their native language as their first. Bahasa Indonesia function as lingua franca that unites 200 various languages over the archipelago.
Vice versa, words of Malay-Indonesian origin also has been borrowed into English. Words borrowed into English (e.g., bamboo, orangutan, dugong, amok) generally entered through Malay language by way of British colonial presence in Malaysia and Singapore, similar to the way the Dutch have been borrowing words from the various native Indonesian languages. One exception is "bantam", derived from the name of the Indonesian province Banten in Western Java (see Oxford American Dictionary, 2005 edition). Another is "lahar" which is Javanese for a volcanic mudflow. Still other words taken into modern English from Malay/Indonesian probably have other origins (e.g., "satay" from Tamil, or "ketchup" from Chinese).
At its development stage, various native terms (mostly Javanese) from all over the archipelago made its way to the language. The Dutch adaptation of the Malay language during colonial period had resulted significant amount of Dutch loanwords and vocabulary. The event significantly impacted the original Malay language which gradually developed into the modern Indonesian language.
The study on Indonesian etymology and loan words reflected its historical and social context. Examples are the early Sanskrit borrowings probably in the Srivijaya period, the borrowings from Arabic and Persian during the time of the establishment of Islam in particular, and the ones from Dutch during the colonial period. Linguistic history and cultural history are clearly linked.
Early Hindu and Buddhist influence from India results in many Sanskrit words in Indonesian (and especially adopted through Javanese influence). Indian traders may have contributed words as well, in Tamil and Sanskrit-related languages.
Indonesian has involved in trade with Chinese since ancient times and also significant of Chinese immigrants began to migrate to Indonesia, as the result some of Chinese language, especially Hokkien dialect being absorbed into Indonesian.
Muslim influence, which came at first through Arabic and Persian traders, over a number of centuries results in an extensive Arabic influence and also Persian.
Portuguese contact, trade and colonization in the 16th century was the first contact between Indonesia and European culture, and had an influence that remains today, in spite of the relatively short time period of that influence.
Dutch colonization and administration, lasting from the 17th century to the 20th, had an extensive impact on the vocabulary. As Dutch-trained linguists determined the rules for the official Indonesian language, Dutch thus had an impact on the structure of the language as well. For example, suffixes such as "-as" (e.g., kwalitas = quality), "-asi" (e.g., administrasi = administration), and "-if" (e.g., fiktif = fictive) were applied with consistency. Some loan words are still intensively used today, although there are genuine Indonesian language.
Modern Indonesian regularly adapts new words from other languages, particularly English. In contrast to the large number of mechanical terms borrowed from Dutch (e.g., automotive parts), hitech words are typically taken from English (e.g., internet).
But the processes may also be ‘out of period’; for example, Indonesian words are still being concocted from Sanskrit, and the influence of the Dutch language certainly continued after the Dutch themselves left.
Indonesian has also generalized brand names into common (lower-case) nouns as generic name. For example, "sanyo" refers to any electrical well pump, regardless of manufacturer or "odol" as all of toothpastes. This is similar to the type of generalization that occurs in English words like "xerox" or "tampax" or "polaroid".
Most of Indonesian languages vocabulary are natively derived from Malay, but some might be ultimately loanwords from Minang language. Yet it is unclear, since Malay and Minang are closely related, and some might consider that Minang language was precursor or old dialect of Malay language.
Compared to Malay language spoken as the native regional language in Sumatra and Malay peninsula, or standardized version of Malaysian language, Indonesian language differ profoundly by large amount of Javanese loanwords incorporated into their already rich vocabulary. This is mostly contributed by Java's position as the center of Indonesian politics, education and culture, since the capital is located in Jakarta on Java island, and large numbers of Javanese reside in capital area. Also large numbers of Javanese as the majority, began to use Indonesian language in their daily conversation, at least in official, formal and educational settings. As the result Javanese began to pour their own vocabularies into Indonesian to describes terms and words that does not have exact counterparts in Malay language. It is important to note that most of Indonesian Sanskrit loanwords are derived and conducted through Old Javanese and Javanese intermediary.
Although Hinduism and Buddhism are no longer the major religions of Indonesia, Sanskrit which was the language vehicle for these religions, is still held in high esteem and is comparable with the status of Latin in English and other Western European languages. Sanskrit is also the main source for neologisms, these are usually formed from Sanskrit roots. For example, the name of Jayapura city (former Hollandia) and Jayawijaya Mountains (former Orange Range) in Indonesian province of Papua were coined in the 1960s, both are Sanskrit origin name to replace its Dutch colonial names. Some Indonesian contemporary medals of honor and awards; such as Bintang Mahaputra medal, Kalpataru award and Adipura award, are also Sanskrit derived names.
The loanwords from Sanskrit cover many aspects of religion, art and everyday life. The Sanskrit influence came from contacts with India long ago before the 1st century. The words are either directly borrowed from India or with the intermediary of the Old Javanese language. In the classical language of Java, Old Javanese, the number of Sanskrit loanwords is far greater. The Old Javanese — English dictionary by prof. P.J. Zoetmulder, S.J. (1982) contains no fewer than 25,500 entries. Almost half are Sanskrit loanwords. Sanskrit loanwords, unlike those from other languages, have entered the basic vocabulary of Indonesian to such an extent that, for many, they are no longer perceived to be foreign.
The loanwords from Arabic are mainly concerned with religion, in particular with Islam. Words of Arabic origin include dunia (from Arabic دنيا dun-ya = the present world, as opposed to the after-life world), kabar (خبر = news), selamat/ salam (سلام salam = a greeting), senin (الإثنين al-Itnain = Monday), selasa (الثلاثاء at-Tulata = Tuesday), jumat (الجمعة al-Jum'at = Friday), hadiah (هدية hadiyyah = gift/present), mungkin (from ممكن mumkin = perhaps), maklum (معلوم ma'lum = understood), kitab (كتاب kitab = book), and kamus (قاموس qamus = dictionary).
Allah is the word for God even in ChristianBible translations. Many early Bible translators, when they came across some unusual Hebrew words or proper names, used the Arabic cognates. In the newer translations this practice is discontinued. They now turn to Greek names or use the original Hebrew Word. For example, the name Jesus was initially translated as 'Isa, but is now spelt as Yesus. Psalms used to be translated as Zabur, the Arabic name, but now it is called Mazmur which corresponds more with Hebrew.
The Chinese loanwords are usually concerned with cuisine, trade or often just exclusively things Chinese. According to the 2000 census, the relative number of people of Chinese descent in Indonesia is almost 1%, although this may likely be an underestimate. Words of Chinese origin (presented here with accompanying Hokkien/ Mandarin pronunciation derivatives as well as traditional and simplified characters) include pisau (匕首 bǐshǒu – knife), mie (麵 > 面 Hokkien mī – noodles), lumpia (潤餅 (Hokkien = lūn-piáⁿ) – springroll), teko (茶壺 > 茶壶 = cháhú [Mandarin], teh-ko [Hokkien] = teapot), 苦力 kuli = 苦 khu (bitter) and 力 li (energy) and even the widely used slang terms gua and lu (from the Hokkien 'goa' 我 and 'lu/li' 你 – meaning 'I/ me' and 'you'). Almost all loan words in Indonesian with Chinese origin comes from Hokkien dialect. Loan words in Indonesian with Chinese origins.
European influence over Indonesian language is significantly influenced through European intervention and colonialism, the most significant evident is the usage of Latin alphabet instead of various local scripts. Portuguese had first arrived in the archipelago and influenced the original Malay language after their conquest of Malacca. The Portuguese dominance over trade in the region and control of the spice island of Moluccas had significantly increase Portuguese influence in trade and also through the introduction of Christianity over the region. The Dutch however shows the most influence in the language, being in control of Indonesia for 300 years after eliminating the Portuguese as a player over control of the archipelago. Dutch language itself wasn't properly introduced over the archipelago before 1799 when the Netherlands' crown took over the colony from the already bankrupt VOC (Dutch East India company), previously the Malay language was adapted by VOC due to its trade and diplomatic benefit which led to mass loanword over the language. English to an extend also have influence over the archipelago's language, being the third most favored foreign language by the educated in the colonial days. English however plays more role over the nation's official language through recent globalization.
Alongside Malay, Portuguese was the lingua franca for trade throughout the archipelago from the sixteenth century through to the early nineteenth century. The Portuguese were among the first westerners to sail east to the "Spice Islands". Loanwords from Portuguese were mainly connected with articles the early European traders and explorers brought to Southeast Asia. Indonesian words derived from Portuguese include sabun (from sabão = soap), meja (from mesa = table), boneka (from boneca = doll), jendela (from janela = window), gereja (from igreja = church), bola (from bola = ball), bendera (from bandeira = flag), roda (from roda = wheel), gagu (from gago = stutterer), sepatu (from sapato = shoe), kereta (from carreta = wagon), bangku (from banco = chair), keju (from queijo = cheese), garpu (from garfo = fork), terigu (from trigo = flour), mentega (from manteiga = butter), and Minggu (from domingo = Sunday).
The former colonial power, the Netherlands, left an extensive vocabulary that can be seen in words such as polisi (from politie = police), kualitas (from kwaliteit = quality), wortel (from wortel = carrot), kamar (from kamer = room, chamber), rokok (from roken = smoking cigarettes), korupsi (from corruptie = corruption), persneling (from versnelling = gear), kantor (from kantoor = office), resleting (from ritssluiting = zipper), kelas (from klas = class), and gratis (from gratis = free). These Dutch loanwords, and also from other non Italo-Iberian, European languages loanwords which came via Dutch, cover all aspects of life. Some Dutch loanwords, having clusters of several consonants, pose difficulties to speakers of Indonesian. This problem is usually solved by insertion of the schwa. For example Dutch schroef[ˈsxruf] → sekrup[səˈkrup]. Many Indonesian vocabulary ending "-i" (ie:administras-i) also are known from the Dutch vocabulary influence "-ie" (ie:administrat-ie). All the months from January (Januari) to December (Desember) used in Indonesian are also derived from Dutch language. It is estimated that Indonesian language today contain 10,000 loan words from Dutch. 
Note: Word after slash means 'genuine' Indonesian language, although may be loans from other language too.
Many English words are adopted in Indonesian through globalization, due to this however many Indonesians mistaken words that were originally adopted from Dutch with English due to the similarity of Germanic traces in both language.
complete (Dutch: Compleet)
modern (Dutch: moderne)
pilot (Dutch: Piloot)
ponsel / HP read:Ha-Pé (shortened word from Hand Phone)
hand phone (used in Singapore, Malaysia, Philippines, and South Korea)
de Vries, Jan W., Grĳns, C.D. and Santa Maria, L. 1983 Indonesian : a check-list of words of European origin in Bahasa Indonesia and traditional Malay Leiden : Koninklĳk Instituut voor Taal-, Land- en Volkenkunde. ISBN 90-6718-004-1.
Badudu, J.S; Kamus Kata-kata Serapan Asing Dalam Bahasa Indonesia; Kompas, Jakarta, 2003