The Singaporean boat captain acquitted of trespassing in Indonesia's waters but still held by local authorities has made an impassioned plea for his freedom.

"I feel that I have spent enough time in lock-up and I have done my punishment, please don't punish me further," said Mr Shoo Chiau Huat during a hearing in a Tanjung Pinang court yesterday.

Mr Shoo was carrying 13 passengers from Singapore and Malaysia on board the MV Selin when the boat was stopped by the Indonesian navy in Tanjung Berakit waters off Bintan island for trespassing on April 16.

All the passengers were deported about a week after their arrests but Mr Shoo was charged with illegal fishing in Indonesian waters.

A court, however, had said there was insufficient evidence and acquitted him in July, but he remains in the custody of local immigration authorities after he was slapped with immigration offences instead.

His lawyer, Mr Suharjo, yesterday appealed to the court to throw out the case against his client on grounds of "irregularity".

The defence lawyer said that the immigration offence faced by Mr Shoo was based on the arrest by the navy, which his client was acquitted of previously.

"This was not a fair trial from the start, and we still do not know the motive behind the navy's move to force this trial," said Mr Suharjo.

The hearing has been adjourned to Oct 18 after the prosecution asked for more time to prepare its response to Mr Suharjo.

A visibly disheartened Mr Shoo, who has been behind bars since April, said he intends to quit his job once he is released.

"This case has been very traumatising, all I did was take people out to sea for fishing, but look what I have been going through," he said. "I'm also worried that my elderly father may find out about this. It will make him feel stressed that I've spent so much time in prison."