The former guerilla leader Taur Matan Ruak is set to replace Jose Ramos-Horta as East Timor's president.

Provisional results on Tuesday from Monday's election gave the former armed forces chief 61 per cent of the votes counted, giving runoff election rival Francisco Guterres only a slim chance of winning the largely ceremonial post for his Fretilin Party.

Ramos-Horta, a Nobel laureate, came third in last month's first round of voting, leaving two contestants in a runoff that proved to be free from violence or claims of vote-rigging.

Both Guterres, a former parliament speaker, and Matan Ruak pledged to abide by the outcome of the balloting and have urged their supporters to do the same.

Matan Ruak, Ramos-Horta and Guterres were independence fighters alongside Xanana Gusmao, East Timor's first president and its current prime minister.

Gusmao, who switched from president to prime minister after the 2007 election, campaigned for Matan Ruak, who is notionally running as an independent.

A win for Matan Ruak would point to another likely loss for Fretilin in the July parliamentary election.

It would show Gusmao still able to win widespread support among the half-island's 620,000 voters for his ruling coalition.

Fretilin formed a government after the former Portuguese colony gained its independence from Indonesia in 2002 but lost power in 2006 amid civil strife that saw international troops return to restore order.

East Timor was a Portuguese colony for 400 years before Indonesia sent in troops in 1975. The 24-year occupation was ended by a UN-sponsored independence referendum in 1999.