Nigeria's main opposition party spokesman said that they are confident of a presidential election win, but worried that the government will interfere with the results as they are collated from thousands of polling stations countrywide.

Confusion and violence blighted Nigeria's tensest presidential election since the end of army rule, with the opposition rejecting results from a turbulent southern state even before they have been announced.

The opposition All Progressives Congress (APC) in Rivers state accused supporters of President Goodluck Jonathan of being behind killings of its campaigners, and denounced the vote there as "a sham and a charade".

APC spokesperson Lai Mohammed said that the ruling party had lost "embarrassingly" even in their strongholds.

"Our major concern now is that these results are not changed at the collation centre or elsewhere. We are not saying this out of fear, we are not saying this out of insecurity, we are saying this out of practical reality.

"We are saying this because we know that the government of the day has lost embarrassingly even in areas where they thought they were going to win, while we have kept all our traditional bases.

"We are very worried and especially because we see some sponsored reports online claiming that the PDP is ahead in some 20 or 23 states which is completely false. We are also worried because we know that some of these sponsored reports are with the knowledge of very top government officials," said Mohammed.

Dismissal of the vote in Rivers - a centre of the Nigerian oil industry - raises the prospect of a disputed national outcome and the risk of a repeat of violence that erupted after the last election in 2011, when 800 people were killed in the mainly Muslim north.

"As and when such a situation occurs, we will not be shy to speak out, put that in the public domain and ask INEC to make the necessary adjustments," Mohammed said.

"Nigerians will simply not want a repeat of what happened 20, 22 years ago and we would just hope that the government would be gracious enough to accept the outcome of these results."

The vote pits Jonathan against former military ruler Muhammadu Buhari.

It is also the first election since the end of military rule in 1999 in which an opposition candidate has a serious chance of unseating the incumbent.

Witnesses said Islamist Boko Haram militants killed more than a dozen voters, while at least two people were shot dead in the oil hub of Port Harcourt, the biggest city in Rivers state which has a long history of political thuggery.

"A lot of feathers have been ruffled in the run up to these elections and I think that will be quite injurious for the nation. I think our first task on winning will be to start healing wounds and that is the very basis for peace and that is the very basis for any progress or development," said Mohammed.

Voting in 28 March election was extended into Sunday at a relatively small number of polling stations after technical glitches hit voter ID machines.

The electoral commission said just 350 polling stations out of 120,000 were still voting.

Turnout appears to have been high, and with up to 56.7 million votes to process, the results could take a while to collate.