Police had last week announced they would provide transport for minority Tamils to return to their homes in the island's embattled northern and eastern regions unless they could prove they were employed in Colombo.
The crackdown is part of efforts to stop the Liberation Tigers of Tamil Eelam (LTTE) infiltrating the city of 600,000 people, police said. There was no immediate comment from the government.
"This operation is a very bad example," Tamil political leader Dharmalingam Sithadthan said.
"It is OK for the LTTE to indulge in this sort of ethnic cleaning because they have no moral responsibility, but a government can't behave like this," he said.
He said the police move reminded him of how the Tamil Tigers had evicted thousands of minority Muslims from the northern peninsula of Jaffna in 1990.
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