Rumsfeld arrived in Kuwait on Sunday on his fourth visit to the region since US-led forces toppled the Iraqi regime of Saddam Hussein last April.
In comments to reporters during a refuelling stop in Shannon, Ireland, Rumsfeld signalled US concern over attempts to drive wedges between the country's Shia, Sunni and Kurdish communities before a planned handover of sovereignty in June.
Asked whether al-Qaida was operating in Iraq, Rumsfeld said, "They are clearly involved and active ... Several things are happening.
"One is a coincidence of interests on the part of terrorist networks, plus former regime elements, plus some criminals.
"Second, some among them are clearly attempting to foment strife between the various religious and ethnic groups in the country, hoping that they will advantage themselves and disadvantage the coalition forces."
A captured letter attributed to Abu Musab al-Zarqawi, a Jordanian with ties to al-Qaida, spells out a strategy of using human bombings against Iraqis to stir-up civil war between Sunni and Shia Muslims before the transfer of sovereignty.
"Experts in the government believe the letter is authentic," Rumsfeld said.
He also noted the presence of the estimated 115,000 US troops in Iraq would "ebb and flow", pulling back from cities where they could and moving back in where Iraqi security forces proved too weak.
Rumsfeld was scheduled to meet with Kuwaiti Prime Minister Shaikh Sabah al-Ahmad al-Sabah and Defence Minister Shaikh Jabir Mubarak al-Sabah on Sunday.
He was also expected to dine in the Gulf state with General John Abizaid and Lieutenant Ricardo Sanchez, the highest US commanders in the region.
His itinerary was kept secret after a spate of attacks on top US officials.
"(There) is a coincidence of interests on the part of terrorist networks, plus former regime elements, plus some criminals. Second, some among them are clearly attempting to foment strife between the various religious and ethnic groups in the country"
US defence secretary
A rocket attack in December struck a hotel where Deputy Defence Minister Paul Wolfowitz was staying, and Abizaid's convoy came under fire in the restive western town of Falluja on 12 February.
Meanwhile, an oil pipeline was hit in southern Iraq on Sunday, while deadly violence flared in the north.
In the first attack of its kind in the south since the collapse of Saddam Hussein's regime last spring, an oil pipeline was targeted near Karbala, 110km from Baghdad, an official Iraqi source said.
"An explosion damaged the pipeline and we don't know who the saboteurs are," said local Karbala official Hamid Salah al-Shabib.
The blast on the Kirkuk-Baghdad-Basra pipeline set off a fire around the site of the attack and thick black smoke could be seen billowing several kilometres away.
Oil pipelines in northern Iraq have been frequently attacked, where a gun battle on Saturday night at the home of a police chief left one Iraqi dead and another seriously wounded.
An Iraqi civilian was also killed on Sunday morning in the northern city of Mosul by a makeshift bomb, planted beside a road used by military convoys.
And police said two bodyguards were wounded when unidentified gunmen opened fire in the city, while in Baghdad three Iraqi policemen were wounded in a bomb blast.