Iraq said on Wednesday there was no evidence to support the report in The New York Times that it was allowing Iran to fly military supplies to Syria through its airspace, but that depends on your interpretation of military supplies.
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Following The Times' report, Iraq confirmed Iran was making the flights, but a government spokesman "said Tehran has assured [Iraqi president Nouri] al-Maliki that the flights are carrying only food and other humanitarian aid to help victims of Syria's civil war," according to the Associated Press's Qassim Abdul-Zahra. But as The Times' Michael Gordon reported, the planes themselves could be seen as military aid. "The Iranians have even provided a cargo plane that the Syrian military can use to ferry men and supplies around the country, according to two American officials," Gordon wrote. Iran is the Syrian regime's closest ally in a region that largely supports the rebels. Senators visiting Iraq said on Wednesday that Iraq letting Iran fly military supplies to Syria through its airspace would damage relations between Washington and Baghdad. But Iraq says it's up to the Americans to prove the flights are actually carrying military supplies, and the evidence in Gordon's report is mostly circumstantial:
One former American official said it was not entirely clear what cargo was being sent to Syria before the flights stopped in March. But because of the type of planes involved, the nature of the carriers and the Iranians’ reluctance to have the planes inspected in Iraq, it was presumed to be tactical military equipment.
Gordon's point is that the United States no longer has the military capability or authority to stop Iran flying over Iraq, and Iraq doesn't have an air force. So for now there's little the United States can do to stop the flights but ask.