Explosions were heard in the majority Tamil city of Jaffna, just hours before polls opened on Tuesday morning.
The Centre for Monitoring Election Violence (CMEV) said there were four explosions but no reports of casualties. It was not immediately clear what caused the blasts.
Jehan Perera, the head of the National Peace Council of Sri Lanka, said that election violence had become commonplace in Sri Lanka since the 1980s and the beginning of the conflict with the Liberation Tigers of Tamil Eelam (LTTE).
"Generally the case is that the ruling party wants to press home its advantage and unleashes its supporters against those of the opposition and the police turn a blind eye," he told Al Jazeera.
"This is not a new practice, but I think on this occasion the violence has been higher than in the previous presidential election but I [also] would not say that this is the most violent election we have seen. We have seen worse elections."
During this election campaign, five people were killed and more than 800 violent incidents were recorded.
Polling stations will close at 4pm (10:30 GMT) and first results are expected to trickle out late on Tuesday, before a final outcome set to be declared on Wednesday.
Tamils in focus
There have been no reliable polls, but both candidates have tried to cash in politically on their popularity among the Sinhalese majority for crushing the LTTE, which had led a 25-year war for a separate Tamil state.
But it is the Tamil minority - those who suffered most from the government offensive against the separatists and who make up more than 12 per cent of the population – who may prove to be kingmakers.
Rajapaksa has campaigned on his war record and his promises to bring development to the nation.
"We defeated terrorism and separatism,'' Rajapaska said in an email to supporters on Monday.
"We are now ready to lead our children and our nation to a brighter future."
Fonseka, who also pledges an economic renaissance, accused Rajapaksa of entrenched corruption and has promised to trim the powers of the presidency and empower parliament if elected.
Neither man has outlined a detailed plan for resolving the grievances of the marginalised Tamil minority that sparked the conflict in the first place.
Benjamin Schonthal, a scholar on Sri Lanka at the US Institute of Peace, told Al Jazeera that the "election is somewhat of an irony".
"You have two candidates who were not particularly associated with minority rights contesting an election which could be decided by minority voters," he said.
"There's been a lot of talk of post-war unity and national reconciliation and promises about assistance to the poor, but at this stage it is unclear what a vote for either candidate would mean."
Twenty other candidates are also running in Tuesday's election, but none are expected to attract a major share of Sri Lanka's 14 million eligible voters.