The 63-year-old CPI-ML (Liberation) Politburo member passed away at around 4:15 am at a party colleague's residence in Chandigarh where he had gone for a meeting, the party said in a statement. Mr Mukherjee is survived by his wife, a son and a daughter.
"Comrade Swapan's loss is an irreparable one - not only for the CPI(ML) but for the entire spectrum of democratic movements. He died as he had lived - active, optimistic, enthusiastic and tireless to the very last," it said.
Lauding Mr Mukherjee, who was in charge of CPI-ML (Liberation) units in Delhi, Punjab, Chandigarh, Maharashtra and Odisha, the party described him as a "brilliant party organiser".
Born on November 17, 1953, Mr Mukherjee had studied at Kirorimal College in Delhi University in the early 1970s, when he was inspired by the Naxalbari struggle to join the Marxist-Leninist movement.
He was actively involved in party work in Delhi since the time of its reorganisation to the second party Congress held in early 1976.
Swapan Mukherjee left Delhi for a brief period from mid-1976 to 1978 around the time of the Emergency and its immediate aftermath to "evade the police witch-hunt", the party said.
Mr Mukherjee also worked in a leading English daily in Delhi while being a member of underground Delhi unit of the party.
In 1987, he quit his job to become a full-time organiser.
He rose to become a member of party's Central Committee in 1993 and later the Politburo.
His body was brought to Delhi from Chandigarh today and will be cremated on Wednesday afternoon, the party said.