Analysts see the election as a referendum on the government's military strategy against the Tamil Tiger rebels.
Rajapaksa formally scrapped a six-year truce in January. The military quickly stepped up its war against the rebels in their northern stronghold, leading to a surge in casualties on both sides and suicide blasts in the capital.
REFUGEES
"There are 300 people in this IDP (Internally Displaced Person) camp, we have been displaced due to the war since 2006, from Muttur, but still we are in this camp," said V Thivakarasa, a 46-year-old carpenter who has been unable to work since fleeing his home.
"I have not received the polling card to vote. I don't want to vote like an IDP, I want to vote in my own village after settling down there."
The Tigers, who are fighting for an independent homeland for Tamils in the north and east, were driven from the east of the island last year, emboldening the government in its aim to finally crush the rebels and rebuild Sri Lanka's economy.
Saturday's elections follow a smaller, dry-run local poll in the east in March, won by a government-backed party made up of the former rebel fighters, who defected from the Tigers in 2004.
Rajapaksa's government has dismissed concerns about the TMVP, who have also been accused of abductions and extrajudicial killings and have yet to lay down their weapons.
A host of other former militant groups who joined the democratic mainstream in the 1980s are also taking part in the poll.
The main opposition United National Party is contesting with the ethnic minority Sri Lanka Muslim Congress and has accused the government of trying to hand over the east to an armed group, despite their pledge to reinstate democracy in the area.
Provincial council elections are held every five years, but elections in the north and east have been repeatedly postponed because of continued fighting since 1988.
