The defence ministry ordered the census to prevent separatist Tamil Tiger rebels from infiltrating the capital.
"Each and every Tamil is not a terrorist.
But 99 percent of the terrorists are Tamils. The security forces have a major problem on their hands to identify terrorists," defence secretary Gotabhaya Rajapakse told local media.
Large crowds queued outside schools, clutching their identification papers, as police personnel took down their details, eyewitnesses said.
"It is impossible for anyone to identify an innocent Tamil from a terrorist until they are apprehended as they all go under the guise of Tamil civilians," said Rajapakse, who is also President Mahinda Rajapakse's younger brother.
Police said hundreds of Tamils had registered on Sunday and that a final tally would be announced later in the day.
The Tigers have been blamed for a string of bomb attacks against public transport in recent months as the military intensified pressure on the rebels' de facto mini-st