"We can disclose evidence that the process is not fair," Fernando "Lasama" de Araujo of the opposition Democrat Party, who finished in third place, said.
In a letter to the national election commission, they complained of a climate of intimidation during polling and called for the count to be stopped.
They said the count should be held in public with all eight presidential candidates and independent observers present.
|Guterres' Fretilin party dominates|
Timorese politics [AFP]
But international monitors have said the poll was generally open, orderly and peaceful despite fears of unrest after gang violence last year left at least 37 people dead.
"The opinion of the EU observation mission in general is that the level of violence and intimidation is not enough to change the opinion of a peaceful and orderly process," Javier Pomes Ruiz, the European Union's chief observer, said.
Ramos-Horta, who won the Nobel prize for championing East Timor's cause during Indonesian occupation between 1974 and 1999, expressed misgivings about the process.
"There are many flaws in the administration of this election," he said.
He said that the United Nations, rather than local officials, should have organised the polls.
He also expressed concerns that a Fretilin victory would damage relations with other countries in the region.
"The Fretilin government has little sensitivity toward the region," he said of the party he founded as a resistance movement.
Along with the outgoing president, Xanana Gusmao - who will run for prime minister in June - Ramos-Horta has been hoping to end Fretilin's dominance of East Timorese politics.
Parliamentary elections will be held on June 30.