Police said arms were recovered from all the three arrested Maoists.
Two sophisticated firearms, including a semi-automatic gun, were recovered from them, the police said. They have been booked under various sections of Arms Act.
The arrest of the trio is said to be a major blow to the Maoists, especially for its urban base. Mukherjee was the prime coordinator between different urban units of the outfit in Kolkata, the North and South 24-Parganas and Howrah districts.
Mukherjee is also one of the most elites of Maoist's leaders. He studied international relations at Jadavpur University and picked up French and Russian. He first came to spotlight for vandalising a showroom selling Tata Motors cars here, during the Singur movement in 2006. The 31-year-old was a close associate of Kishenji.
In Mar 2010, there were rumours that Mukherjee was killed during a gunfight between the security forces and the guerrilla squad guarding Kishenji.