Some 16,000 officials would gather information from 14,000 villages nationwide from today until December 20.
"The government has nothing to hide. A lot of people have come out with various accusations with their own figures. We will come out with real facts," P B Abeykoon, Secretary to the Ministry of Public Administration said.
Sri Lanka, since the end of the ethnic conflict four years ago, has faced accusations of ignoring international calls for accountability over alleged 40,000 civilian deaths.
Census chief D C A Gunawardena said, "The terrorist conflicts, political and any such conflicts that have occurred during 1982 and after wards are considered as internal conflicts for the purpose of this census."
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Asked if the census data would provide verification to the figure of 40,000 which international rights organizations including the UN had accused Sri Lankan troops of killing in the last stages of the war, Abeykoon said, "Why should we go for a census if we have anything to hide. We are trying to get a clear picture for ourselves."
The move comes after the Commonwealth summit this month was overshadowed by allegations of atrocities by government troops in the final stages of the conflict in May 2009.
International pressure led to the leaders of Canada, India and Mauritius boycotting the summit in protest against Colombo's human rights record.
British Prime Minister David Cameron attended the summit but infuriated Sri Lanka by visiting the war-torn Tamil-dominated Jaffna region in the north.
After meeting with survivors, Cameron warned that he would push for an international probe unless Sri Lanka conducts a credible inquiry of its own by March.