The move came a day after NCP President Sharad Pawar pointed the needle of suspicion.
In a significant development, the Maharashtra government will conduct a parallel investigation into the Elgar Parishad - Koregaon-Bhima case, a senior state minister said on Monday.
Nationalist Congress Party national spokesperson and Minister for Minority Affairs Nawab Malik said that the state government will set up a Special Investigation Team (SIT) to probe the sensitive case soon.
A decision on this will be taken soon by state Home Minister Anil Deshmukh, he added, four days after the Pune Sessions Court assigned the case to the National Investigation Agency (NIA).
The move came a day after NCP President Sharad Pawar pointed the needle of suspicion by stating that Centre had handed over the case to the NIA as the previous Bharatiya Janata Party government in the state "wants to hide something".
"There appears to be something that the former (Devendra) Fadnavis government wants to suppress. That's why the probe has been handed over to the NIA. The Fadnavis government was in power when the Koregaon-Bhima violence broke out," Mr Pawar told mediapersons in Jalgaon on Sunday.
However, he said the chief minister was within rights to use his discretionary powers and it was the Centre's prerogative to investigate the matter, "but the Maha Vikas Aghadi government should have been taken into confidence".'
The Elgar Parishad - Koregaon-Bhima case has been a bone of contention between the Centre and Maharashtra and created huge friction between the ruling allies Shiv Sena, and NCP-Congress since the past three weeks.
The row erupted after Mr Pawar shot off a letter to the state government last month, demanding a separate probe into the role of the Pune Police which had investigated the matter, and barely a couple of days after that, the Centre ordered the NIA to take over the case.