The operative, whose name was not provided, works for Abu Musab Zarqawi, a senior associate of Osama bin Laden, the official said, speaking on condition of anonymity.
The capture occurred this week, the official said.
Zarqawi, linked to the death of an American diplomat in Jordan last year, is one of the Bush administration's links between al Qaeda and the regime of Saddam Hussein. He is also among the administration's most-wanted al Qaeda figures.
Zarqawi fled Afghanistan during the U.S.-led war to oust the Taliban. He passed through Iran and then received medical treatment in Baghdad in mid-2002, U.S. officials have said.
During this time, several of his associates, affiliated with Egyptian Islamic Jihad, joined him in the city. The Egyptian Islamic Jihad is considered merged with al Qaeda.
It is unclear if the captured operative was one of those associates.
Zarqawi left Baghdad, but those associates remained, officials have said. His current whereabouts are unknown.
Officials suspect Zarqawi is linked to a plan to use poison against European targets late last year. They also say he took part in a foiled plot to bomb a tourist hotel in Amman, Jordan, during millennium celebrations.
There was no early word on where the Zarqawi associate might be taken. Many captives of the war in Afghanistan were brought to Guantanamo Bay, Cuba, for interrogation and detention.
The arrest of Zarqawi's associate is the second reported major terrorist capture of the war in Iraq. On April 15, U.S. forces nabbed Abu Abbas, the alleged mastermind of the 1985 Achille Lauro hijacking in which an American tourist was killed.
Iraq's alleged links to terrorism were a major part of the Bush administration's case for was with Iraq, along with the claim — as yet unproven — that Iraq possessed weapons of mass destruction.
The administration used one argument to amplify the other: if Iraq were connected to terror groups, that meant any weapons it had could be passed on to stateless, violent organizations.
In a February presentation to the United Nations Security Council that outlined the U.S. case for war, Secretary of State Colin Powell alleged that Zarqawi had helped establish an explosive and poisons training center in northeastern Iraq.
Both Zarqawi and the captured man are also suspected of links to Ansar al-Islam, an Islamic extremist group in northern Iraq composed of ethnic Kurds.
The alleged poison camp was in the area controlled by Ansar al-Islam. The group's camps were bombed heavily by U.S. forces during the war. It is has not been confirmed that the site was used for developing poisons.
Powell also alleged that Zaraqwi's operatives in Baghdad controlled "the movement of people, money and supplies into and throughout Iraq for his network."
Documents discovered recently in the bombed out headquarters of Iraq's intelligence service provide evidence of a direct link between Saddam Hussein's regime and bin Laden's terrorist network, a newspaper reported Sunday.
Papers found Saturday by journalists working for the Sunday Telegraph reveal that an al Qaeda envoy met with officials in Baghdad in March 1998, the newspaper reported.
The paper said the documents show that the purpose of the meeting was to establish a relationship between Baghdad and al Qaeda based on their mutual hatred of the United States and Saudi Arabia.
The meeting went so well that it was extended by a week and ended with arrangements being discussed for bin Laden to visit Baghdad, the newspaper said.
That report appears to contradict another claim of Powell's — that "going back to the early and mid-1990s when bin Laden was based in Sudan, an al Qaeda source tells us that Saddam and bin Laden reached an understanding that al Qaeda would no longer support activities against Baghdad."
That contact would have predated the 1998 meeting, which was intended to establish a relationship.