Hundreds of Tamils were expelled from the city on Thursday by the government.
They have arrived in a town close to the front line that divides government and Tamil Tiger rebel-held territory.
A defence ministry spokesman said nearly 400 Tamils were expelled because they were part of a plot by rebels to set off bombs in Colombo.
The police have offered no evidence against any of the evicted Tamils.
The Supreme Court’s interim order came after a non-governmental organisation Centre for Policy Alternatives filed a complaint that the police action was a violation of fundamental rights.
"The court will hear the case on 22 June and in the meantime, the police inspector general has been restrained from carrying out any evictions of Tamils," news agency AFP quoted a court official as saying.
Human rights group The Free Media Movement in Sri Lanka has condemned the expulsions saying they are tantamount to ethnic cleansing.
Police said that Tamils who were in the capital "without valid reasons" were made to board buses bound for the north and east of the island on Thursday.
The police said the crackdown was part of continuing efforts to stop the Tamil Tigers infiltrating the capital city of 600,000 people.
They also said the measure was bei