Thousands of people marched peacefully through the Honduran capital Tegucigalpa on Sunday to support opposition presidential candidate Xiomara Castro.

The electoral court has declared conservative Juan Orlando Hernandez of the ruling National Party as the winner.

The court said that with 99 per cent of ballots counted, Mr Hernandez had 37 per cent and Ms Castro was second with 29 per cent.

Ms Castro and her husband - former president Manuel Zelaya - led the protest march in a car carrying the body of a Libre Party activist who had been shot only dead hours before the demonstration.

"We are here to denounce the culture of death promoted since the coup. This can only be a political crime," said Mr Zelaya.

Libre Party supporter Jose Ardon was kidnapped late on Saturday and was found dead hours later.

He was leader of a group of bikers who have led the marches in support of Mr Zelaya and his wife since the 2009 coup.

Mr Zelaya called for a vote-by-vote recount and said that as head of the Libre Party he will file a complaint with the electoral tribunal.

"If they do not accept our complaint, we will go to the courts, and if the courts don't take our case, we will go to international bodies," Mr Zelaya said.

The party alleges that voting tally sheets were altered, dead or absent people were included on the electoral roll and inadequate monitoring of polling stations allowed for fraud.