"The court granted leave to proceed with the case," a court official told AFP.
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Fonseka was arrested on Monday, two weeks after being trounced in presidential elections by the incumbent, President Mahinda Rajapakse. His detention triggered violent protests in Colombo and other parts of Sri Lanka.
The defence ministry says he is to be court-martialled on unspecified charges of conspiring against the government.
A lawyer for Fonseka said they regarded the supreme court decision to take up the petition as a major victory.
Hundreds of Fonseka supporters packed the courtroom, while police manned barricades outside.
Anti-riot squads had been put on alert after violent clashes Wednesday outside the court complex between Fonseka loyalists and ruling party activists.
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Members of the elite Special Task Force comma