Voting at some 850 stations began on schedule amid tight security to elect the first post-war provincial administration in the region dominated by the LTTE until their defeat in 2009.
Soldiers were patrolling the streets with police, election observers said.
More than 2,000 local and foreign observers were deployed in the province where nearly 715,000 people are eligible to vote in the election which would elect a 36-member northern provincial council for a five-year term.
The run-up to the election has seen allegations of army intimidation. But this has been firmly denied by the authorities.
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There are nearly 906 candidates for the polls in northern council which is witnessing its first ever elections after councils were created under the 13th Amendment, a byproduct of the 1987 Indo-Lanka Accord.
In the first north and east provincial council elections held in 1988, only one political party participated due to the LTTE's armed campaign to set up a separate Tamil homeland.
"The Election Commissioner's Office is doing its best under difficult circumstances, but is handicapped by an outdated system in need of reform, compounded by inadequate funds.
"Yet, the systematic misuse of State resources, notably of the Ministry of Economic Development, to benefit pro-government candidates, and the deliberate violation of election law through combining development activities with election campaigning have irreparably flawed the democratic process in the Mullaitivu District," the CMEV stated in its pre-poll report on the Mullaitivu which is one of the five northern districts.