He obtained a PhD in Social Sciences from the Australian National University, thus becoming the first Papua New Guinean to earn a PhD of any kind. In 1986, he was the first Papua New Guinean to be appointed Professor, and became head of the History department at the University of Papua New Guinea. He has published a number of articles on the history, culture and politics of his country. His book A Short History of Papua New Guinea was first published in 1993.
In 1992, Waiko was elected to Parliament, beginning his national political career. He was Minister for Foreign Affairs from 2001 to 2002, before losing his seat in Parliament in the June 2002 general election. In the 2007 general election, he stood unsuccessfully for election at the Sohe Open constituency, representing the new Papua New Guinea Party.
Waiko was controversially involved with a prominent Malaysian businessmen in the logging industry in Papua New Guinea, Philip Lee. After Lee had "fraudulently obtained three Papua New Guinea passports and was found guilty of violating PNG immigration laws", Foreign Affairs Minister John Pundari ordered his deportation. Pundari was sacked by Prime Minister Mekere Morauta, and replaced by Waiko, who suspended and reviewed the deportation order. When it was revealed in February 2002 that Waiko and Lee "held shares in the same company", and Waiko admitted they were "business partners", PNG Forest Watch expressed its concern over a "clear conflict of interest" and urged Waiko to resign. Papua New Guinea's Trade Union Congress also called for Waiko to be sacked.
Waiko has been the subject of two biographical films. He was the subject of, starred in, and was associate producer of, the 1990 film Man Without Pigs, by Chris Owen. In 2007, he starred in Minister Without Money, a short film by Sandra Welkerling, focused on his political career, set against the wider context of Papua New Guinean politics.
- Waiko, John D., A Short History of Papua New Guinea, 1993, ISBN 0-19-553164-7. Biographical information on back cover.
- "Man Without Pigs", Documentary Educational Resources
- Bibliography of John Waiko in G. W. Trompf, PaybackThe Logic of Retribution in Melanesian Religions, 1994, ISBN 0-521-41691-4, p.524
- "Nationalism and Papua New Guinea Writing", Australian Quarterly, 1971
- PNG Electoral Commission, 2007
- Ron Crocombe, Asia in the Pacific Islands: Replacing the West, Suva: IPS Publications, 2007, ISBN 978-982-02-0388-4, p.183
- "Forest pressure move", Post Courier, 19 February 2002
- "PNG TUC wants minister sacked", Radio Australia, 13 February 2002
- "PNG illegal passports scam", Radio Australia, 30 August 2002
- "Man Without Pigs (1990)", New York Times
- Australian Film Commission, Australian government website