Human Rights Watch (HRW) said Robinson's departure followed pressure from the United States and others for her to leave because she had spoken out on issues such as the death penalty.
"She has paid a price for her willingness to confront publicly big governments like the United States when they violate human rights," HRW's Reed Brody said.
"Mary Robinson has set a standard of candor and energy for future high commissioners. We will be sad to lose her as an ally," he said.
Asked to comment at a press conference, Robinson said she did not want to comment on the positions of individual countries but said she was aware many supporters wanted her to stay on.
She was focussed on an "intensive and very constructive" coming six months, she said, adding she had no plans except to stay in the area of international human rights.
Robinson said the acts of September 11 had also been an attack on the "very system of international relations on which this commission and the entire work of the United Nations is based."
"I have a sense that respect for the international human rights norms and standards is at some risk," she told reporters.
"It's an important opportunity for the commission, as the lead body in human rights, to reassert very vigorously and firmly the importance of adhering to international human rights standards, while combating terrorism particularly in the aftermath of the 11th of September," she said.
The high commissioner has already warned that the war on the terrorism is taking a heavy toll on civil liberties and urged countries to redouble efforts to safeguard citizens basic rights.
For the first time in the commission's 56-year history, it opened without the US on its members' list after it was voted off last year under a system to ensure a rotation of members.
Washington will however have observer status at the talks due to examine violations around the world, including Israel and the Palestinian territories, China, Chechnya, African countries and Colombia.
We place Maggie Thatcher and her on opposite sides of a debate table, roll the cameras, and see who wins after one hour.
I'll wager a month's salary that Thatcher would have this socialist weeping for "fairness" in about 5 minutes.