John Martinkus was born in Australia in 1969 and grew up in Melbourne. He studied international relations at Melbourne's La Trobe University. Following a period studying Russian Language in Moscow he visited East Timor and in late 1994 began writing freelance stories about the conflict, which he sold to papers in Australia and New Zealand.
In 1997 he was one of only a few journalists who managed to interview the Falintil pro-independence guerillas in the mountains of East Timor under occupation, including the commander David Alex who was ambushed and killed by the Indonesians less than six months later. He returned again in mid 1997 to report on Alex's capture and death.
Martinkus returned to East Timor in mid 1998 and remained there until after independence in mid 2000, after which he wrote his first book on the conflict. In that period in East Timor he worked for Associated Press, Australian Associated Press, Fairfax, The Bulletin and several international papers as well as writing A Dirty Little War on the conflict in East Timor (Random House 2001). The book was shortlisted for the New South Wales Premier Awards and Martinkus was nominated for A Walkley award for his AAP coverage of the violence in 1999. Five separate visits over a period of three years resulted in the book Indonesia's Secret War in Aceh (Random House 2004), which provides an unprecedented and comprehensive account of the conflict in Aceh as the Indonesian military sought to hide it from the outside world until they finally closed down reporting from the province with Martial law in mid 2003.
In 2004 Martinkus spent February and March travelling in Iraq under American-led occupation. In October that year he was kidnapped outside his hotel in Baghdad by Sunni Insurgents who released him 24 hours later after using the internet to verify his status as a journalist.