Tamil officials said the census ordered by President Mahinda Rajapakse last month would give a distorted picture because of its "flawed" terms of reference, arguing that a more credible alternative was needed.
"The council will work out the logistics of taking a count," Dharmalingam Sithadthan, a senior member of the Northern Provincial Council, told AFP from the regional capital Jaffna.
"This is something we have to do because we don't accept the government census."
The Rajapakse government kicked off its own census late November after disputes over the scale of the killings in the final phases of the war dominated a Commonwealth summit in Colombo earlier in the month.
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Sri Lanka has repeatedly rejected allegations that its troops killed civilians while battling the separatist Liberation Tigers of Tamil Eelam, who were also accused of using civilians as a human shield.
While launching the government census in November, the head of the public administration ministry, P.B Abeykoon, said they had "nothing to hide".
Compilers of the census would only be able to ask survivors whether they had lost spouses, sons or daughters and would not be allowed to ask survivors about the fate of their parents, said Premachandran.
The census would also lack any input about casualties from survivors who have sought refuge.
"We strongly believe this is an attempt to give lower figures for war fatalities," Premachandran said.
"For planning purposes of the council, we want the actual numbers, not watered down figures," he added.
Rajapakse, who is a member of the majority Sinhalese community, has rejected proposals for international investigators to conduct their own separate inquiry.