The Pune police have claimed the conclave was backed by Maoists.
A court in Pune hearing the Elgar Parishad case on Friday passed an order to transfer the case to a special NIA court in Mumbai.
Additional Sessions Judge SR Navander passed the order.
Before the judge passed the order, the prosecution submitted an application stating that they do not have any objection to the National Investigation Agency's plea seeking transfer of the case.
The Centre had last month transferred the probe into the case from the Pune Police to the NIA, a move then criticised by the Shiv Sena-NCP-Congress government.
The NIA had submitted the application before the court in the last week of January.
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 charged by the NIA in the Elgar Parishad case.