Martinho Gusmao, spokesman for the commission, said: "With this percentage, there will probably be a second round."
A majority of at least one vote above 50 per cent is needed to win and if the figures do not change significantly, a run-off will be held on May 8 between the top two candidates.
A final tally is due to be released on April 19, if there is no appeal.
The election is seen as a gauge of support for a plan by Ramos-Horta and his close ally, Xanana Gusmao, the outgoing president who will run for the more powerful post of prime minister in June general elections, to seize control of parliament from the Fretilin party.
Fretilin official Jose Manuel Fernandes said their own tally from polling stations nationwide showed 40 per cent of votes counted had gone to their candidate.
Ramos-Horta won the 1996 Nobel Peace Prize for championing East Timor's struggle to end decades of brutal Indonesian rule.
Although by far the best-known of the eight candidates, turnout at his recent election campaign rallies was lower than expected.
East Timor declared independence from Indonesia in 2002 but descended into chaos last year after Mari Alkatiri, the then-prime minister, fired 600 soldiers - about one-third of the country's army - provoking gun battles between rival security forces that spiralled into gang warfare and looting.
At least 37 people were killed and some 155,000 displaced before the government collapsed.
Tens of thousands of refugees have yet to return home, and the country remains desperately poor, with a 50 per cent unemployment rate.
East Timor was a Portuguese colony for more than three centuries before it was invaded by Indonesia in 1976.
Guerrillas spent the next 24 years fighting the occupation, a struggle Ramos-Horta championed from exile.
In the country's first election for independence in 1999, Indonesian troops and their militia allies killed more than 1,000 people and burned hundreds of homes and businesses.