Speaking to reporters during a previously unannounced trip to Baghdad, Kerry said that he and Iraqi Prime Minister Nouri al-Maliki had engaged in "a very spirited discussion" on the Iranian flights, which U.S. officials believe are ferrying weapons and fighters intended for the embattled Syrian government.
Kerry said the plane shipments -- along with material being trucked across Iraqi territory from Iran to Syria -- were helping President Bashar Assad's regime cling to power by increasing their ability to strike at Syrian rebels and opposition figures demanding Assad's ouster.
"I made it very clear that for those of us who are engaged in an effort to see President Assad step down and to see a democratic process take hold ... anything that supports President Assad is problematic," Kerry said at a news conference at the U.S. Embassy in Baghdad after meeting separately with Maliki at his office. "And I made it very clear to the Prime Minister that the overflights from Iran are, in fact, helping to sustain President Assad and his regime."
The overflights in Iraq have long been a source of contention between the U.S. and Iraq. Iraq and Iran claim the flights are carrying humanitarian goods, but American officials say they are confident that the planes are being used to arm the support the Assad regime. The administration is warning Iraq that unless action is taken, Iraq will be excluded from the international discussion about Syria's political future.
U.S. officials say that in the absence of a complete ban on flights, Washington would at least like the planes to land and be inspected in Iraq to ensure that they are carrying humanitarian supplies. Former Secretary of State Hillary Rodham Clinton secured a pledge from Iraq to inspect the flights last year, but since then only two aircraft have been checked by Iraqi authorities, according to U.S. officials.
One senior U.S. official traveling with Kerry said the sheer number of overflights, which occur "close to daily," along with shipments trucked to Syria from Iran through Iraq, was inconsistent with claims they are only carrying humanitarian supplies. The official said it was in Iraq's interest to prevent the situation in Syria from deteriorating further, particularly as there are fears that al-Qaida-linked extremists may gain a foothold in the country as the Assad regime falters.
The official, who spoke on condition of anonymity because the official was not authorized to speak publicly on the matter, said there are clear links between al-Qaida linked extremists operating in Syria and militants who are also carrying out terrorist attacks in Iraqi territory with increasing regularity.
Kerry's comments in Baghdad come as U.S. lawmakers are calling for President Barack Obama to do more to stop the bloodshed in Syria, including possible airstrikes against Assad's aircraft fleet.
The Republican chairman of the House Intelligence Committee, Rep. Mike Rogers of Michigan, said Sunday the U.S. should create a "safe zone" in northern Syria that would give the U.S. more leverage with opposition forces.
"This doesn't mean the 101st Airborne Division and ships" are deployed, Rogers told CBS' "Face the Nation." "It means small groups with special capabilities re-engaging the opposition so we can vet them, train them, equip them so they can be an effective fighting force."
Last week, Sens. Carl Levin, D-Mich., and John McCain, R-Ariz., asked Obama in a letter to step up U.S. military efforts in the region, including destroying Assad's aircraft using precision airstrikes.
Kerry said Iraq's tacit approval of Iranian overflights left the American people wondering how an ally would undermine U.S. efforts, particularly after the enormous sacrifices made by the United States in liberating Iraq from Saddam Hussein's tyrannical rule.
"There are members of Congress and people in America who increasingly are watching what Iraq is doing and wondering how it is that a partner in the efforts for democracy and a partner for whom Americans feel they have tried so hard to be helpful, how that country can be, in fact, doing something that makes it more difficult to achieve our common goals, the goal expressed by the prime minister with respect to Syria and President Assad," he said.
In addition to the overflights, Kerry said he had urged Maliki and other Iraqi officials to promote unity amid a spike in sectarian violence and called on them to ensure that upcoming provincial elections are free and fair. Kerry said the postponement of the polls in two provinces -- Anbar and Ninevah -- was unacceptable and should be reversed.
"We strongly urge the prime minister to take this issue to the cabinet and to see if it can be revisited, because we believe very strongly that everybody needs to vote simultaneously," he said.
In addition to his meeting with Maliki, Kerry saw Iraqi parliament speaker parliament speaker Osama al-Nujaifi, a Sunni, whose faction is at odds with Maliki's Shiia. Kerry also spoke by phone with Massoud Barzani, the head of the Kurdish Regional Government based in Irbil to encourage the Kurds not go ahead with unilateral actions -- especially involving oil, like a pipeline deal with Turkey.
Kerry arrived in Baghdad from Amman, where he had been accompanying President Barack Obama on his tour of Israel, the Palestinian Authority and Jordan. His visit to Iraq is the first by a U.S. secretary of state since Clinton went in April 2009. During Obama's first term, the Iraq portfolio was largely delegated to Vice President Joe Biden as Obama wound down the war.