WASHINGTON — As America’s generals prepare for an increase in troops in Iraq, the American intelligence community has been fiercely debating the extent to which operatives directed by Iran’s security services have penetrated the Iraqi government.

Several lists containing names of suspected moles have been circulating in the intelligence community since December, according to one American diplomat and two American intelligence officials who spoke on condition of anonymity. But the names of the suspected Iranian agents themselves are the focus of a heated dispute.

This debate, among others concerning Iran’s influence and control of Iraqi government institutions, is one key factor holding up the publication of a consensus intelligence finding on Iraq known as a National Intelligence Estimate. The dispute over Iranian power in Iraq’s Interior Ministry, national military, customs office, Health Ministry, and Defense Ministry will determine how President Bush’s troop surge is implemented, one intelligence official said. “This could lead to disbanding whole units of the Iraqi military and affect how we embed our guys in their units,” the official said. “If it’s true, if some of this is true, it’s very bad. But we don’t know yet.” While the intelligence community is divided over the degree of Iran’s influence in the Iraqi government, the Bush administration has changed its earlier assessment of Tehran’s aims in Iraq.

At a hearing before the Senate Select Committee on Intelligence earlier this month, the outgoing director of national intelligence, John Negroponte, said the old view was that Iran does not want a civil war in Iraq. But he said this assessment was changing.

“One has to wonder why it is that they have increased their supply of these kinds of lethal weapons to extremist Shia groups in Iraq, provoking violence, attacks on coalition forces, and others. And one wonders if their policy towards Iraq may not have shifted to a more aggressive posture than it has been in the past,” he said.

Iran’s intentions in Iraq were explored in a paper released this month by a former Army translator and current analyst for the Fort Leavenworth, Kan.-based Foreign Military Studies Office, a U.S. Army branch that works largely with open source material for analysis of foreign militaries. In the paper, “Iran’s Contribution to the Civil War in Iraq,” Mounir Elkhamri says Iran’s Quds Force has worked to create a rump Shiite state in southern Iraq since shortly after the attacks of September 11, 2001, and that the Shiite militias killing Sunni civilians in Iraq are working at the behest of Iranian intelligence and Revolutionary Guard.

Documents captured from Saddam Hussein’s intelligence service show “Iran’s deep penetration in Iraqi society and institutions. Iran clandestinely supported the U.S. invasion of Iraq and took measures to turn it to her advantage,” Mr. Elkhamri writes in the paper, published by a Washington-based national security think tank that includes both Democrats and Republicans on its board, the Jamestown Foundation.

While the Iranians were helpful in the invasion period, Mr. Elkhamri writes, by as early as 2004 the Iranian Quds Force and Ministry of Intelligence and Security began establishing influence to advance Tehran’s interests. On March 11, 2004, Quds Force, the arm of the Iranian Revolutionary Guard in charge of terrorism against America and Israel, opened the “Office to Help Poor Iraqi Shia.”

By offering an upfront gift of $2,000 and a monthly stipend of $1,000, the office was able to recruit 70,000 young Shiite men in 2004 to join one of the numerous militias allied with Iran, Mr. Elkhamri writes.

Mr. Elkhamri’s conclusions are stark. “Today in Iraq, Shia militias — death squads loyal to Iran — have successfully infiltrated the new Iraqi security forces at all levels. They have also expanded their area of operations throughout Iraq. They are responsible for more civilian deaths than the Sunni and foreign insurgents who are the United States’ number one enemies in Iraq. These militias — the Mahdi Army, the Badr Brigade, and others — are carrying out attacks under the authority of and in the uniforms of the Iraqi Ministry of the Interior and the Ministry of Defense.”

Several analysts, asked this week for their impressions of Mr. Elkhamri’s paper, expressed skepticism about some of his claims. “The paper points to a number of activities that Iran is up to in Iraq, many of which are potentially harmful to the course of reconstruction,” the director for research at the Saban Center for Middle East Studies at the Brookings Institution, Kenneth Pollack, said. “However, the sourcing leaves much to be desired, and a number of statements are factually incorrect. Beyond that, many of its claims are simply interpretations that don’t necessarily stand up to the evidence that is available.”

The director of regional strategic programs at the Nixon Center, Geoffrey Kemp, said: “He makes a convincing case that the Iranians are deeply embedded in many levels of Iraqi society and government. However, he assumes that the Iraqi Shia share the same agenda as the mullahs. While it is true they have common shortterm goals, in the long run it would be unwise to conclude that Shia in Iraq will become part of Iran’s aspiring empire. The Iraqi Shia community is not monolithic, and many resent Iranian pretensions and behavior.”