Munde, whose party is a key ally in the Shiv Sena-led Maha Vikas Aghadi government, has made the demand in a letter written to Thackeray on Monday.
Koregaon-Bhima case: Bombay HC refuses to quash case against Gautam Navlakha, wants thorough investigation
The bench dismissed the petition filed by Navlakha seeking to quash the FIR lodged against him by the Pune police in January 2018.
The Delhi HC freed Navlakha from house arrest saying the Supreme Court last week had given him the liberty to approach the appropriate forum within four weeks to seek further recourse.
The Maharashtra police had arrested the five activists on August 28 in connection with an FIR lodged following a conclave.