MUMBAI: In a change of stand, the Maharashtra government has said it has no objection to the National Investigation Agency (NIA) taking over probe into the Elgar Parishad case, in which human rights activists have been arrested for alleged links with Maoists.

Additional chief secretary (Home) Sanjay Kumar told PTI on Thursday that "the state home department has no objection to the case being entrusted to the NIA".

Home minister Anil Deshmukh sought to put the ball in the court of chief minister Uddhav Thackeray , who belongs to the Shiv Sena, the lead constituent in the ruling Maha Vikas Aghadi which also consists of the NCP and the Congress.

Talking to reporters here, Deshmukh, an NCP leader, said "The state agencies were investigating the Koregaon Bhima (Elgar Parishad) case. But, the Centre handed over the investigation to the NIA.

"As home minister, my stand was that the Centre should have taken the state government into confidence before taking the decision. We were putting up our stand in the court in this direction. The chief minister has the right to overrule my stand."

The Centre last month transferred the probe in the case from the Pune Police to the NIA, a move then criticised by the Shiv Sena-NCP-Congress government.

Deshmukh had then publicly expressed disapproval of the Centre's move and termed it as against the Constitution.

The volte-face on the issue appears to have brought to the fore differences between the Chief Minister's Office and the home department led by Deshmukh over the high-profile case.

Deshmukh said the court in Pune will give its order (on transfer of the case) on Friday.

"We will take the advocate general's opinion on setting up of an SIT to probe the Elgar case as demanded by (NCP chief) Sharad Pawar and whether the state government can proceed with setting up of the SIT," he said.

Last week, Thackeray had criticised the Centre's decision, saying the Union government has all rights to step into the probe, but it should have taken the state into confidence before handing over the investigation to the NIA.

He said the case was handed over to the NIA at a time when Pawar was demanding constitution of a Special Investigation Team (SIT).

The NIA last week filed an application before a sessions court in Pune, seeking transfer of case papers, seized data, court records and proceedings to the special NIA court in Mumbai.

However, the prosecution had then opposed the NIA's application, saying the reasons given by the central agency in its plea were not legal and sufficient to transfer the case to the special NIA court.

"The offence is committed within the jurisdiction of the local court (Pune); chargesheet has filed and draft charges have been also filed and the matter is fixed for framing of charges," the prosecution had said in its response.

The case relates to alleged inflammatory speeches delivered at the Elgar Parishad conclave, held at Shaniwarwada in Pune on December 31, 2017, which the police claimed, triggered violence near the Koregaon-Bhima war memorial in the district the next day.

The Pune police have claimed the conclave was backed by Maoists.

During the probe, the police arrested Left-leaning activists Sudhir Dhawale, Rona Wilson, Surendra Gadling, Mahesh Raut , Shoma Sen, Arun Ferreira, Vernon Gonsalves , Sudha Bharadwaj and Varavara Rao for alleged Maoist links.

These nine activists, currently in jail, are among 11 people booked by the NIA in the Elgar Parishad case.

While the Pune police had applied IPC section 124A (sedition) in the case, the NIA FIR does not have this charge.

Similarly, IPC sections like 121 (waging or attempting to war or abetting waging war against the Government of India), 121A (conspiracy to commit offences punishable under section 121) and 120B (criminal conspiracy) were missing from the NIA's FIR.

The accused have been charged under IPC sections 153 A (promoting enmity between groups ), 505 (1)(b) (with intent to cause, or which is likely to cause, fear or alarm to the public), 117 (abetting commission of offence by the public or by more than ten persons) among others and certain sections of the anti-terror act UAPA.

