Analysts say this is one of Sri Lanka's most critical polls as the two main candidates have such differing views on the peace process.
Voters affected by the tsunami are expected to play a key role in the outcome.
Road blocks in Tamil Tiger controlled areas contributed to the low turn there.
Heightened security in Batticaloa district in eastern Sri Lanka, but not many voters.
Presidential candidate Mahinda Rajapakse has pledged a hard line in peace talks with the Tamil Tigers.
Opposition leader and presidential candidate Ranil Wickramasinghe was the prime minister when a ceasefire was reached with the Tigers 2002.