"A sitting high court judge will head the inquiry," Mr Fadnavis said, a day after a youth died as a group, opposed to the celebrations due to the "British victory" in the battle, clashed with Dalits rallying their way to the battle memorial.
The violence sparked off protests in various parts of the state today, including in Mumbai where protesters staged a rail roko in Chembur.
Shops and business establishments were shut and a senior journalist of a national news channel was attacked as groups of youths from Chembur, Vikhroli, Mankhurd and Govandi joined the protest, police said.
The incident of violence in Pune district would be probed by a sitting judge, Mr Fadnavis said, adding that Rs 10 lakh compensation would be given to kin of the youth killed.
The youth's death would be probed by the CID, Mr Fadnavis told reporters.
He appealed for calm and peace, saying Maharashtra is a progressive state which does not believe in casteist violence.
Strict action would be taken against those who use social media to spread rumours, he said and appealed to political parties to refrain from saying anything that would fuel tensions.
Yesterday's event was to mark 200th anniversary of the Bhima-Koregaon battle in Pune district, in which forces of the East India Company had defeated Peshwa's army.
Dalit leaders commemorate the British victory, as it is believed that soldiers from the Mahar community -- then considered untouchable -- were part of the East India Company's forces.
However, some right-wing groups in Pune had expressed opposition to the celebrations of the "British victory".
The violence had erupted after a local group and some members of the crowd on its way to the memorial had an argument over some issues.