A three-member panel of apex court judges probing the allegations had earlier indicted Ganguly of "unwelcome behaviour".
West Bengal Chief Minister Mamata Banerjee wrote twice to President Mukherjee for taking urgent n1ecessary action, so as to remove Ganguly from the post of WBHRC chief at the earliest.
Banerjee's Trinamool Congress, a section of the legal fraternity, several women's organisations and civil rights groups had also spearheaded a nationwide clamour for his resignation.
However, former Lok Sabha speaker Somnath Chatterjee had stood by Ganguly.
Known as an upright judge during his 18-year tenure with various high courts and then the Supreme Court, Ganguly had given a number of landmark verdicts that nailed the high and the mighty.
Just before he retired, Ganguly ordered cancellation of 122 2G licences granted by then telecom minister A. Raja in 2008 due to financial irregularities.
Responding to Ganguly's decision vto quit, former attorney general Soli Sorabjee said: "When he talked to me yesterday over telephone, he said 'I am contemplating resignation'. I told him that's the right thing to do. Today he has resigned. But I think the media was unfair to him."
Additional Solicitor General Indira Jaisingh, who had been at the forefront of the demand that Ganguly demit office, said: "It is the right step. When such allegations are leveled against people holding such august offices, they should not hold on to them."
National Women's Commission chairperson Mamta Sharma said: "It would have looked more diginified had he resigned when the allegation was leveled. Better late than never. But I have a feeling that had there been no pressure, he would not have resigned."
Congress leader Rashid Alvi said: "He should have put in his papers earlier. After lot of pressure, he has resigned."
Bharatiya Janata Party (BJP) leader Prakash Javadekar said" "We had made this demand in the Lok Sabha. The girl's complaint is a serious matter. At last he has resigned. But it was long overdue."
Trinamool MP Kalyan Bandopadhay: "Irrespective of parties, everybody was demanding his resignation. I think it was India's view that he resign."
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