The development has become a sore point in Maharashtra, with the Uddhav Thackeray-led Maha Vikas Aghadi hitting out at the Bharatiya Janata Party (BJP) led central government for not consulting with it before taking away the probe from the state police and handing it over to NIA.
The Pune police, which was probing the case, had found letters and documents which allegedly suggested a plot to assassinate Prime Minister Narendra Modi.
Last week, the Supreme Court reserved a judgment on a challenge raised by the Maharashtra government against a Bombay High Court decision refusing the state police a 90-day extension to complete its investigation and file charge sheet against those accused of Maoist links in the aftermath of the Bhima-Koregaon violence.
On 1 January, 2018, the day marking bicentenary celebrations of the Bhima Koregaon battle, violence broke out in Pune's Shanivarwada, leading to one death and injuries to several others.
Police had then arrested several activists with alleged "Maoist links". The Pune police alleged that they funded the Elgar Parishad meeting on 31 December 2017, where inflammatory speeches had led to the violence the next day.
The police subsequently arrested, on 28 August 2019, writer and poet Varavara Rao, lawyer and activist Sudha Bhardwaj, academic and activist Vernon Gonsalves, and human rights activists Arun Ferreira and Gautam Navlakha, for alleged Maoist links.