The report emerged as the two governments are in delicate negotiations over the future of American troops in Iraq. Those talks have already extended past their July 31 deadline and have drawn sharp criticism from Iraqis who want an end to the U.S. presence.
Critics may well use the allegation to step up pressure on the government not to sign a deal or hold out for the most favorable terms.
Iraqi government spokesman Ali al-Dabbagh said Baghdad will raise the allegations with the U.S. and ask for an explanation. But if true, he warned, it shows a lack of trust.
"It reflects also that the institutions in the United States are used to spy on their friends and their enemies in the same way," al-Dabbagh said in a statement.
"If it is true, it casts a shadow on the future relations with such institutions," al-Dabbagh added, referring to the CIA and other U.S. intelligence agencies.
In Washington, the White House declined to directly comment on the allegations. Instead, spokeswoman Dana Perino said official channels of communication between the two governments happen daily.
"We have a good idea of what Prime Minister Maliki is thinking because he tells us, very frankly and very candidly, as often as we can," Perino said.
Despite the Iraqi government's sharp public criticism, a top aide to al-Maliki was more measured in his response.
"If this is true, then we feel sorry about that. We look upon the Americans as our partners. There's nothing of real value that would require the Americans to spy on us. On top of that, we have nothing to hide from the Americans to make them have to spy on us," the aide told The Associated Press. He spoke on condition of anonymity because of the sensitivity of the issue.
Other Iraqi officials expressed dismay about spying allegations.
"If it is true, it is very dangerous and we will condemn it because how can a friend spy on you? This is unacceptable for us," said Mahmoud Othman, a prominent Kurdish lawmaker.
One lawmaker from the largest Shiite bloc even warned that the allegations could influence security agreement talks.
If true, it could "reflect negatively on the current negotiations on the agreement," said Abbas al-Bayati of the United Iraqi Alliance.
The U.S.-Iraq security pact will determine the future status of the U.S. military in Iraq after the current U.N. mandate expires at the end of the year. Officials from both sides have said a draft agreement would see American troops leave Iraqi cities as soon as June 30.
But there are several sticking points between the two sides.
Iraqis want the U.S. to commit to taking all forces out by the end of 2011. Bush, though, has long resisted a timetable for pulling troops out of Iraq.
Other key issues also remain unresolved including the issue of legal jurisdiction over Americans in Iraq, as the Iraqi forces assume greater responsibility. It was unclear how the spying allegations would affect those talks.
Even before the spying allegations surfaced, several Iraqi factions had been expressing deep concern about details of the draft agreement.
A spokesman for the Iraqi Accordance Front - the largest Sunni bloc in parliament - warned Friday against the U.S. pulling its troops out of the cities too early.
Sunnis are particularly concerned that they don't trust the mostly Shiite army and police. They also fear Shiite militias and Iran, the predominantly Shiite neighbor, would wield too much sway in Iraq's mostly Shiite government after the Americans leave.
"There are political forces who welcome the withdrawal of American troops from Iraq, but there are also fears from other forces of the possibility that militias and al-Qaida might activate again and ... some neighboring countries would snatch this opportunity to dominate their presence in the Iraqi arena," Salim Abdullah al-Jubouri told the U.S.-funded Radio Sawa.
Anti-American Shiite cleric Muqtada al-Sadr's followers, meanwhile, fear the deal will bind the U.S. and Iraq in a long-term security relationship, instead of restoring Iraqi sovereignty.
Al-Sadr is in Iran, but still retains considerable political clout back home. Sadrist clerics at Friday prayers in the Baghdad slum of Sadr City and the southern city of Kufa denounced the agreement.
"The suspicious agreement is a permanent occupation of Iraq," read a banner held by one worshipper during a march in Kufa.
In Iran's capital, prayer leader Ayatollah Ahmad Jannati also advised Iraq not to "bow to humiliation" by signing a pact with the U.S., the state-run news agency, IRNA, reported.
"If you accept the agreement, Americans will never leave the country then," he told worshippers.
Associated Press reporters Saad Abdul-Kadir and Qassim Abdul-Zahra contributed to this report.