In 1687 Father Ventimiglia, a Theatine, was commissioned by Pope Innocent XI to preach Christianity in Borneo. There are no memorials of this mission, which has left no traces in the island although the missionary declared that God had blessed his labours.
The Propaganda congregation decreed on 27 August 1855 the erection of the northern part of the island of Borneo into an independent prefecture of North Borneo and Labuan and entrusted it to the Rev. Carlos Cuarteron, a Spaniard. Father Cuarteron was originally a sea-captain and had vowed, after escaping great peril, to devote himself to the evangelisation of Borneo. He landed at Labuan in 1857, in company with several missionaries who deserted him in 1860. Although alone in the island of Labuan, Father Cuarteron courageously continued his labours. At length, seeing that isolation made him powerless, he went to Rome in 1879 to request that the Propaganda place the mission in charge of an institute. From Rome Father Cuarteron went to Spain, where he soon died.
The island of Labuan has an area of 30 square miles (78 km2) and contains 6,800 inhabitants; it is an important shipping station between Singapore and Hong Kong. The prefect Apostolic lives at Labuan. The stations served are Labuan and Kuching (Sarawak), the two most important towns. Outside of these two places where the missionaries live ten stations are visited: Sibu, Kanowit, Igan, Oya, Mukah, Baram, Papar, Jesselton, Putatan, and Sandakan. According to the " Missions-Atlas " of P. Streit, the statistics of the Catholic mission in the early 20th century were: 19 regular priests, 2 lay brothers, 15 sisters; 8 churches; 20 chapels; 16 catechists; 14 schools with 740 pupils; 2,600 baptisms; about 1,000 catechumens.
The British had obtained the island of Labuan in 1846; they gradually extended their power over the petty rulers of the northern part of Borneo until, in 1888, the British protectorate of North Borneo was formally acknowledged. English speaking missionaries being desired in the British part of Borneo, the Propaganda (19 March 1881) confided the mission of North Borneo and Labuan to the Society for Foreign Missions of Mill Hill, from England. The first prefect Apostolic appointed under the new administration was the Rev. Thomas Jackson. The society continued in charge of the mission.