The 112 Indian fishermen, who were produced before a Jaffna Magistrate, were remanded to judicial custody for 14 days.
According to one official, the court wants the legal process completed ahead of their release.
Hectic diplomatic efforts are on to secure an early release of the fishermen. Wednesday and Thursday are holidays here – Thursday is Poya Day (full moon), sacred for Buddhists.
Earlier in the afternoon, there was hope that the fishermen would be freed by Wednesday evening.
But formalities could not be completed in time and the stand of the court has now made it impossible to explore the legal option ahead of Friday.
According to Indian consulate officials in Jaffna, the 112 fishermen are being held along with 18 trawlers.
The Indian High Commission is trying to get an early release and has been in touch with the Sri Lankan authorities, including its Attorney General Mohan Peires.
The Indian fishermen were apprehended by the Tamil fishermen of Jaffna, the Sri Lankan Navy claimed, 15-20 km off Point Pedro and then later handed over to the police there.
On Wednesday night 24 fishermen in four boats were secured by the Sri Lankan authorities.