Saquib Nachan, charged with engineering a bomb blast in a train in Mulund, on Thursday surrendered before the Bombay high court.
Justices Ranjana Desai and S K Shah ordered the police to take the accused in their custody.
The judges were hearing a petition filed by his father alleging that cops might kill Nachan in a fake encounter.
Nachan denied he was absconding and said he was in his village at Padgha in Shahpur taluka.
The petitioner's lawyer, Mubin Solkar, said that on March 27, policemen had gone to his village to arrest him, but the villagers prevented them from doing so.
The next day, three Lashkar-e-tayiba terrorists were killed in an encounter by the two cops who had come to Padgha.
He said the accused was ready to surrender and cooperate with police.
Although Nachan had spent ten years in Ahmedabad jail for offences under the Terrorist and Disruptive Activities [Prevention] Act, this could not be cited as a ground for arrest in the blast case, the lawyer said.
