Annan's spokesman, Fred Eckhard, said al-Akhdar al-Ibrahimi was expressing his own personal views when he said Tel Aviv was complicating the search for an interim Iraqi government.
"The secretary-general's views, as expressed over the last seven years, do not contain the word 'poison'", Eckhard said.
Israel's UN mission said it was "disturbed" by al-Ibrahimi's statements, saying a UN official should not voice personal opinions - especially when they contradicted UN policy.
Al-Akhdar al-Ibrahimi told French radio there was a link between Israeli actions and the recent upsurge of violence in Iraq.
He said the handover of power in Iraq was being complicated by Israel's policies in the West Bank and Gaza.
Al-Ibrahimi said his job was made more difficult by Israel's "violent and repressive security policy" and its "determination to occupy more and more Palestinian territory".
"There are lots of other people on this planet ... they [the US] should make an effort to learn how to live with them"
UN special envoy
He added that people's perception in the region was of the "injustice" of Israeli policy compounded by the "thoughtless support" of the US.
Message to America
Al-Ibrahimi also urged the US to start negotiating with Annan about the UN's role after the 30 June handover to a new US-approved Iraqi goverment.
He said the US had to learn how to live with a world in which it was the only superpower.
"There are lots of other people on this planet," he said. "They [the US] should make an effort to learn how to live with them."