Al-Akhdar al-Ibrahimi, the former Algerian foreign minister, told a news conference at the UN Ayat Allah Ali al-Sistani sent a written message through an aide to UN Secretary-General Kofi Annan "a few days ago" saying he had nothing to do with negative press reports from some members of the Iraqi Governing Council.
Al-Ibrahimi went to Baghdad last month with a UN team to study the feasibility of holding elections before June and to discuss proposals for an interim government when the US-led occupation ends on 30 June.
He quoted al-Sistani as saying, "As I told Mr Brahimi, we do want the UN to play a role in Iraq."
The note from al-Sistani denied he had anything to do with the criticism of al-Ibrahimi and the UN, most of which came from former exile leader Ahmad Chalabi, a member of the Iraqi Governing Council close to the US Defence Department.
But al-Ibrahimi said he did not know when he would return to Iraq and was waiting for a formal invitation from the US-led occupation authorities and the 25-member Governing Council.
"I don't think it is so much a credibility problem for the UN as internal politics in Iraq"
The about-face by Chalabi and others is of concern to the US whose officials in Baghdad and Washington have asked the United Nations to help give legitimacy to an interim Iraqi government that is to take power by 30 June.
Annan, speaking to reporters before al-Ibrahimi's news conference, said he made it clear "we are prepared to go back and assist should they want us to do so and I am waiting for them to let us know."
"I don't think it is so much a credibility problem for the UN as internal politics in Iraq," he added.
Several Shia members of the Governing Council have expressed reservations about al-Ibrahimi, a Sunni Arab with a secular, nationalist background.
Photos have circulated of al-Ibrahimi shaking hands with Saddam Hussein, in an apparent effort to discredit the diplomat. Al-Ibrahimi in 1998 set up a visit between Annan and Saddam Hussein, although it was not known if the photos were authentic.
A spokesman for Chalabi said the United Nations had opposed "the liberation of Iraq" and mishandled the oil-for-food programme, put in place to alleviate the impact of sanctions.