Kerry told reporters at a news conference he informed Prime Minister Nouri al-Maliki in a meeting Sunday -- which was not announced publicly before it was held -- Iranian flights to Syria over Iraqi airspace were "problematic."
"I made it very clear to the prime minister that the overflights from Iran are, in fact, helping to sustain President [Bashar] Assad and his regime," Kerry said after a meeting with Maliki in Baghdad, the first by a U.S. secretary of state since 2009.
"I also made it clear to him that there are members of Congress and people in America who are increasingly watching what Iraq is doing," Kerry said at a news conference that Maliki did not attend.
U.S. lawmakers are monitoring Iranian overflights and could block Washington's assistance to Iraq, which amounts to $1.7 billion this fiscal year, U.S. officials have said.
Kerry said Sunday he argued in his "spirited" meeting with Maliki that Iraq ought to have a role in international discussions about Syria's post-Assad future but he said to secure that role, it was important Iraq stop facilitating aid for Assad.
"We agreed to try to provide more information with respect to this," Kerry said, a comment The New York Times said referred to Baghdad's insistence Washington share U.S. intelligence with Iraq on the Iranian flights to show they were carrying arms.
The Obama administration has been unable to persuade Iraq to block overflights from Iran or even to perform regular inspections.
The Times reported in September Iran resumed shipping military supplies to Syria, using a route that takes their planes through Iraqi airspace.
Citing senior U.S. officials it did not name, the newspaper said Iraq at the time was both reluctant and unable to stop the flights despite pressure from Washington, which is leading an international effort to impose sanctions on the Assad regime.
Baghdad maintains the Iranian planes are delivering humanitarian support.
A senior official traveling with Kerry, whose name was not reported, told journalists the number of overflights "is, in itself, an indication that these can't possibly be only humanitarian flights." The official said Kerry was convinced the flights included "weapons and fighters and that this is absolutely contrary to the international goals with Syria and is dangerous for Iraq."
Iran has emerged as one of Maliki's closest regional allies, The Wall Street Journal said, pointing to a shared alarm in Baghdad and Tehran about the largely Sunni insurgency in Syria seeking to overthrow Assad.
Baghdad and Tehran are Shiite-dominant governments.