The CWC meeting witnessed some emotional moments with members telling Mukherjee, who has been chosen as the UPA Presidential candidate, that he will be missed.
Prime Minister Manmohan Singh, Congress President Sonia Gandhi and Defence Minister A K Antony praised Mukherjee for his contribution to the party.
Recalling his long association with the CWC, the highest decision making body of the party, Mukherjee thanked the party for all the cooperation and for nominating him for the president's post, sources said.
He became a member of the CWC in 1978 and has been a key player in the top decision making body of the party.
Sweets were distributed at the CWC meeting while Congress leaders wished the 76-year-old leader a good innings.
Mukherjee, who is likely to resign tomorrow from the post of Finance Minister, did not step down from the CWC or any of the party posts he holds. Party sources said he may do so later.
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Known for his razor sharp intellect, Mukherjee, a quintessential Congressman, is variously described as a walking encyclopedia, chronicler of Congress history, expert in matters of Constitution and governance and a stickler for rules in Parliament.
Mukherjee is likely to file his papers for the Presidential elections on June 28.
Congress General Secretary Digvijay Singh was not present at the CWC meeting.
Asked about his absence, he said, "I am in Madhya Pradesh to attend a private function. I have informed my party leadership. It was a pre-scheduled meeting in my constituency".