Two senior Bush administration figures, Defence Secretary Donald Rumsfeld and National Security Adviser Condoleezza Rice, made the allegations - without giving detailed information to back them up.
They said that Washington had evidence that Baghdad had been providing al-Qaeda operatives with training in the development of chemical weapons.
"We do have solid evidence of the presence in Iraq of al-Qaeda members, including some that have been in Baghdad," Mr Rumsfeld said.
"We have what we consider to be very reliable reporting of senior-level contacts going back a decade and of possible chemical and biological agent training," he added.
Questioned by reporters on how recent the information was, he said that the information was "current".
Ms Rice told American television that the US Government did not contend that Iraq was behind the 11 September attacks on New York and Washington.
But she said Iraqi President Saddam Hussein had a long history of links with terrorism, and there were some al-Qaeda personnel who had found refuge in Baghdad.
The secret ties between Baghdad and Osama Bin Laden's terror network were "a story that is unfolding, and it is getting clear, and we're learning more," she added.
"We clearly know that there... have been contacts between senior Iraqi officials and members of al-Qaeda, going back for actually quite a long time.
"We know too that several of the detainees [at the American naval base in Guantanamo Bay] - in particular some high-ranking detainees, have said that Iraq provided some training to al-Qaeda in chemical weapons development."
'Hard to assess'
BBC News Online world affairs correspondent Paul Reynolds says the allegations by the Bush administration are hard to assess.
If true, they would lay a legal basis for unilateral action by the US against Iraq, under the self-defence provisions of the United Nations Charter.
Correspondents say Ms Rice's and Mr Rumsfeld comments mark the first time that the Bush administration has tried to substantiate its claim that Iraq has a working relationship with the al-Qaeda network.
A dossier on Iraq's weapons of mass destruction published this week by the British Government made no mention of any links between Baghdad and al-Qaeda.