The report also said all such shipments from Iran through Turkey have ceased. Earlier this month, US officials said they were questioning Iraq about Iranian flights in Iraqi airspace suspected of ferrying arms to Assad, a staunch Iranian ally. On Wednesday, US Senator John Kerry threatened to review US aid to Baghdad if it does not halt such overflights.
Iraq says it does not allow the passage of any weapons through its airspace. But an intelligence report obtained by Reuters says Iranian weapons have been flowing into Syria via Iraq in large quantities. Such transfers, the report says, are organized by the Islamic Revolutionary Guard Corps.
"This is part of a revised Iranian modus operandi that US officials have only recently addressed publicly, following previous statements to the contrary," said the report, a copy of which was provided by a UN diplomatic source.
"It also flies in the face of declarations by Iraqi officials," it said. "Planes are flying from Iran to Syria via Iraq on an almost daily basis, carrying IRGC (Iranian Revolutionary Guard Corps) personnel and tens of tons of weapons to arm the Syrian security forces and militias fighting against the rebels."
Although the specific charges about Iraq allowing Iran to transfer arms to Damascus are not new, the intelligence report alleges that the extent of such shipments is far greater than has been publicly acknowledged, and much more systematic, thanks an agreement between senior Iraqi and Iranian officials.
Iraqi officials in Baghdad and New York did not have any immediate comment.
The issue of Iranian arms shipments to Syria came up repeatedly at a Senate hearing in Washington on Wednesday on the nomination of Robert Beecroft as the next US ambassador to Baghdad. Beecroft is currently deputy chief of mission there.
John Kerry, the Democratic chair of the Senate Foreign Relations Committee, asked Beecroft what the embassy was doing to persuade the Iraqis to prevent Iran from using their airspace for flights carrying weapons to Syria. Beecroft said that he and other US officials made clear to Iraq the flights must stop.
Kerry said he was alarmed that US efforts thus far had not persuaded Baghdad to halt the overflights, and suggested that the United States could in future make some of the hundreds of millions of dollars in assistance it gives to Iraq contingent on their cooperation on Syria.
"Maybe we should make some of our assistance or some of our support contingent on some kind of appropriate response," he said. "It just seems completely inappropriate that we're trying to help build democracy, support them, put American lives on the line, money into the country, and they're working against our interest so overtly."
The intelligence report, which Western diplomats said was credible and consistent with their information, said Iran had cut a deal with Iraq to use its airspace.
One envoy said it was possible that Tehran and Baghdad did not in fact have any formal agreement, only an informal understanding not to raise questions about possible arms transfers to Syria.
In comments published by Iranian media on Sunday, Mohammad Ali Jafari said members of the IRGC were providing non-military assistance in Syria and Lebanon. He added that Tehran might get involved militarily in Syria if its closest ally came under attack. A day later, however, Iran's foreign ministry denied those remarks.
Two Boeing 747 aircraft specifically mentioned in the intelligence report as being involved in Syria arms transfers - an Iran Air plane with the tail number EP-ICD and Mahan Air's EP-MNE - were among 117 aircraft hit with sanctions on Wednesday by the US Treasury Department.
The Treasury Department also blacklisted aircraft operated by Iran's Yas Air for supplying Syria with weapons. A UN panel of experts that monitors compliance with UN sanctions against Iran has repeatedly named Yas Air, along with Iran Air, as supplier of arms to Syria.
The Treasury Department statement on the new blacklistings said the move would "make it easier for interested parties to keep track of this blocked property, and more difficult for Iran to use deceptive practices to try to evade sanctions."
The statement did not mention Iraq.
Earlier this year, the UN panel of experts recommended that Yas Air be put on the UN blacklist for helping Iran skirt a UN arms embargo. So far the Security Council has not taken any action on that recommendation.
The UN panel's reports have described Iranian arms shipments to Syria via Turkey, not Iraq.
The intelligence report said such transfers across Turkish airspace had ceased.
"Since Ankara adopted a firm position against Syria, and declared that it would intercept all weapons shipments sent to the Assad regime through Turkish territory or airspace, Tehran has all but completely stopped using this channel," it said.
Tehran is forbidden from selling weapons under a UN arms embargo, which is part of broader sanctions against Iran over its nuclear program.
Earlier this month, UN Secretary-General Ban Ki-moon said Syria's conflict had taken a brutal turn with other countries arming both sides, spreading misery and risking "unintended consequences as the fighting intensifies and spreads."