Special public prosecutor advocate Yug Chowdhary said he has resigned. He is the second prosecutor to tender resignation in the last two years.
"Yes I have resigned from the case," Chowdhary said, without attributing any reason for his move.
In 2013, advocate R B Mokashi had resigned and so far, only one witness has been examined in the case.
Those facing trial are former encounter specialist Sachin Vaze, Rajendra Tiwari, Rajaram Nikam and Sunil Desai.
Police claimed that he escaped after the vehicle in which he was being taken to Aurangabad met with an accident at Jategoan in January 2003.
But co-accused in the case, Dr Abdul Mateen, had claimed that Yunus died due to torture in custody.
Later, a complaint was filed against Yunus in Parner police station.
Yunus's father Sayyed Khwaja Ayub alleged that his son was killed in police custody and filed a habeas corpus petition in the Bombay high court.
The high court also ordered CID to close the FIR filed by Vaze, which had said that Yunus had escaped, as CID found that the complaint was false.
Later, CID filed a new FIR on the basis of statement given by Mateen who said that Yunus was tortured to death.
After investigations, CID filed a charge sheet against the four accused, though it had pointed fingers at 14 police officers for the custodial death.
The state government also sanctioned prosecution of only four accused.
The session court had in March 2001 framed charges against the accused on charges of murder and criminal conspiracy, beside other sections of Indian Penal Code.
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