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Two officials of the Maharashtra ATS on Thursday left the special court in Mumbai which is conducting the trial of the 2008 Malegaon blast case after the defence lawyers objected to their presence.
The Anti-Terrorism Squad had probed the case initially before the National Investigation Agency took it over.
When two ATS officials turned up in the court on Thursday on the Maharashtra government's directions, the NIA lawyer said the agency did not have any intimation in this regard.
Advocate J P Mishra, a defence lawyer, contended that these officers were not authorised to attend the trial.
As per the law, the NIA can take help of another probe agency during investigation but not during a trial, the defence lawyer said.
When Judge P R Sitre asked the two officials about their presence, they said they were sent by ATS chief Vineet Agarwal on the directions of Maharashtra Home Minister Dilip Walse-Patil.
They only had oral instructions and no written order, they informed the court.
When the defence lawyers said they would not proceed if the ATS officials remained present, the duo left the court room.
They would file an application (seeking permission to attend) at the next hearing, they told the judge before leaving.
Taking note of several prosecution witnesses turning hostile in the case, Home Minister Walse-Patil had last week said ATS officials would attend the trial.
Six people were killed and over 100 injured when an explosive device strapped to a motorcycle went off near a mosque in Malegaon, a communally sensitive town in north Maharashtra, on September 29, 2008.
Pragya Singh Thakur, the Bharatiya Janata Party member of Parliament from Bhopal, is among the accused.