Mukherjee was arrested upon entering Kashmir on 11 May 1953. He and two of his arrested companions were first taken to Central Jail of Srinagar. Later they were transferred to a cottage outside the city. Mukherjee's condition started deteriorating and he started feeling pain in the back and high temperature on the night between 19 and 20 June. He was diagnosed with dry pleurisy from which he had also suffered in 1937 and 1944. The doctor prescribed him a streptomycin injection and powders, however, Mukherjee informed him that his family physician had told him that streptomycin did not suit his system. The doctor, however, told him that new information about the drug had come to light and assured him that he would be fine. On 22 June, he felt pain in the heart region, started perspiring and started feeling like he was fainting. He was later shifted to a hospital and provisionally diagnosed with a heart attack. He died a day later. The state government declared that he had died on 23 June at 3:40 a.m. due to a heart attack.