Ivory Coast's electoral commission has said opposition candidate Alassane Ouattara has won the presidential run-off but the Constitutional Council has contested the announcement.
The BBC's John James in the main city Abidjan says there will now be a tug of war between the two bodies with the outcome unclear.
Supporters of President Laurent Gbagbo had tried to block the result, saying there had been fraud in the north.
Former rebels control this area.
It is also where Mr Ouattara is most popular.
The election is intended to reunify the world's largest cocoa producer.
The announcement of the result of Sunday's run-off had been much delayed, leading to heightened tension in the country.
The electoral commission head, Youssouf Bakayoko, said Mr Ouattara had won 54% of the vote, compared to 46% for Mr Gbagbo.
He was speaking under armed guard at a hotel, rather than from the commission's headquarters.
About the same time the head of the Constitutional Council, Paul Yao N'Dre, who is seen as being close to Mr Gbagbo, said it was taking over the declaration from the election commission.
"Because of disagreements on the results of some regions, the independent electoral commission wasn't able to give the provisional results.
"The Constitutional Council - responsible for sorting out disputes in presidential elections - finds itself in charge, to find a solution to the disagreements, and proclaim the definitive presidential election results," Mr N'Dre said.
An office of Mr Ouattara's RDR party was attacked in Abidjan on Wednesday night, leaving at least four people dead - just an hour before the deadline to release the election results and despite a curfew.
An RDR official told the BBC that some of the assailants were wearing civilians clothes, others in gendarme uniform. There has been no independent confirmation that gendarmes were linked to the attack.
Officials from Mr Gbagbo's FPI party say one of their local offices was subsequently attacked in an apparent revenge raid.
Both the army and UN peacekeepers have been patrolling Abidjan's streets since Sunday to prevent an outbreak of violence.