Indonesian prosecutors on Tuesday (April 4) tendered fresh charges against Singaporean fishing boat captain Shoo Chiau Huat.

He was charged with sailing in Indonesia's waters in April last year without a permit under the country's shipping laws.

The move came even though he pleaded guilty in January and recently paid a 50 million rupiah (S$5,300) fine for entering Indonesia illegally for the same incident which led to his arrest.

Shoo did not enter a plea on Tuesday but he will have to decide whether to go to trial or plead guilty to the offences which carries a maximum penalty of one year in jail.

Shoo had seven Singaporeans and six Malaysians on board MV Selin when the boat was stopped by the Indonesian Navy on April 16 last year in Tanjung Berakit waters, off Bintan island.

The 50-year-old has been in remand for almost a year, even though he was acquitted of the original offence of illegal fishing in July last year.

This was because he was slapped with immigration offences after his acquittal for illegal fishing.

He decided to plead guilty to the charge of entering Indonesia illegally in January and paid the fine last month in hope of being released - but he now faces what he fears would be another long trial.

His extended detention prompted Singapore's Ministry of Foreign Affairs (MFA) to send a diplomatic note to their Indonesian counterparts late last year.

The MFA in a statement on Tuesday after the hearing said that it was deeply concerned over the long-drawn judicial process against Shoo and his prolonged detention in Indonesia.

The ministry said it has been in constant contact with the Indonesian authorities since Shoo's detention to ensure that he is accorded his due legal rights under Indonesian law.

"The Singapore Government respects the laws and judicial process of Indonesia in connection with Mr Shoo's case, but remains deeply concerned over his prolonged detention and long-drawn judicial process," said the MFA spokesman. "We will continue to reiterate to the Indonesian authorities that Mr Shoo's case be processed expeditiously, so that he can return to Singapore without further delay."

MFA also said its officers from the Singapore Consulate in Batam will continue to render all necessary consular assistance to Shoo and his family.

It also reminded Singaporeans operating pleasure crafts, recreational fishing vessels and yachts, as well as Singaporeans engaging in business activities in Indonesia, to familiarise themselves with Indonesian laws and the judicial process.