"I voluntarily opt out of that position, and don't want to continue as a member of the guest facility and be a burden on NUJS," Ganguly said in his letter to NUJS Vice Chancellor P. Ishwara Bhat.
The NUJS Thursday said it had dissociated itself from Ganguly since the allegation came up.
I voluntarily opt out of that position: Justice AK Ganguly
"Since the matter came up, he has not been part of the university framework," an NUJS spokesperson said.
Faculty members had last month asked the university to sever relations with Ganguly.
Ganguly, currently chairman of the West Bengal Human Rights Commission, also suffered a big setback Thursday as the union cabinet cleared the home ministry's proposal for a presidential reference to the Supreme Court for a probe into the allegations.
The proposal will be sent to President Pranab Mukherjee, who will then forward the matter to the chief justice of India, seeking a probe into the issue.
A three-member SC panel probing the allegations had earlier indicted Ganguly of "unwelcome behaviour".
There has been a nationwide clamour for Ganguly to step down as head of the rights panel, but the retired judge has steadfastly refused.
In a letter to Chief Justice of India P. Sathasivam, he alleged that there was a palpable design to malign him because of the judgments he had given against "powerful quarters".
West Bengal Chief Minister Mamata Banerjee and other leaders of the ruling Trinamool Congress have been demanding that Ganguly quit the post.
However, former Lok Sabha speaker Somnath Chatterjee has stood by the former judge.