Jonathan, who assumed office last year after the death of President Umaru Yar'Adua, received more than half of the votes cast in an April election, beating his primary challenger Gen. Muhammadu Buhari by about 10 million votes, according to an independent election commission.
Tony Momoh, chairman of the opposition Congress for Progressive Change, told Bloomberg News the results were a farce and should be nullified.
"The results announced to the world were manipulated, where the elections took place, between the polling units and the collation centers," he was quoted as saying.
Riots broke out in the predominantly Muslim north after news that Jonathan, a Christian, defeated Buhari, a Muslim.
Post-election conflicts in Nigeria displaced tens of thousands of people and injured more than 400.
Past elections were marred by significant violence and around 50 people were killed during the prelude to the April election.