Police said before the trial started, the accused had pleaded 'not guilty', and now they could not be allowed to change their stand when the trial was reaching its end.
"We told the court that there should be no deviation from the procedure, no subsequent plea can be accepted," said special public prosecutor Ranjit Sangle.
The prosecution also said this application should be decided only at the time of recording of the statements of accused at the end of the trial.
He also said the application pleading guilty did not say that the accused would not challenge the court's verdict in the high court (if convicted).
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The court is likely to hear further arguments on the application next week.
The Indian Navy arrested a total of 120 Somali pirates between January and March 2011 by intercepting their boats, and rescued Thai and Myanmarese hostages.
The accused are being tried for offences under relevant sections of Indian Penal Code, Arms Act and Unlawful Activities Prevention Act. One of them died during the trial.