Samuel Berger, under investigation for removing classified documents, has resigned as adviser to Democratic presidential candidate John Kerry.
John Kerry (left) said Berger served his nation "with honour"
Mr Berger, who was national security adviser to former US President Bill Clinton, took secret papers from the National Archives.
He has admitted inadvertently taking copies of a classified memo while preparing to address the 9/11 inquiry.
He has said it was "an honest mistake" and voiced "deep regret".
Mr Berger was acting as an informal adviser on foreign policy matters to John Kerry.
Mr Kerry said he supported Mr Berger's decision to leave the campaign.
"Sandy Berger is my friend and he has tirelessly served this nation with honour and distinction," he said.
"I respect his decision to step aside as an adviser to this campaign until this matter is resolved objectively and fairly."
The bipartisan commission investigating the 11 September 2001 terror attacks on New York and Washington is due to deliver its final report on Thursday.
Mr Berger testified in March before the commission, which has examined all aspects of the attacks.
As Mr Clinton's national security adviser, he was questioned about the Clinton administration's response to the al-Qaeda threat.
In preparation for his testimony, he reviewed thousands of pages of classified terrorism and security documents in a secure reading room at the National Archives in Washington.
It was during this work, according to Mr Berger and his lawyers, that he removed notes he had made about the anti-terror papers he consulted.
He also inadvertently took copies of actual documents.
He returned them all, but some copies of a 1999 intelligence report on terrorist plots to disrupt the millennium celebrations are still missing. Mr Berger believes he may have inadvertently discarded them.
"I deeply regret the sloppiness involved but I had no intention of withholding documents from the commission, and to the contrary, to my knowledge, every document requested by the commission from the Clinton administration was produced," Mr Berger said in a statement to the Associated Press.
Mr Berger's lawyer, Lanny Breuer, says his client has offered to co-operate fully with the investigation and has not yet been charged with anything.
Mr Berger served as President Clinton's national security adviser from 1997 to 2001.