Tehran on Tuesday asked Iraq not to stop and search its Syria-bound aircraft despite US pressure to do so, after Baghdad inspected Iranian planes twice this month.
"The Iraqi government should resist such pressures and do not allow such acts to take place in the future," said Iranian foreign ministry spokesman Ramin Mehmanparast.
The Iraqi authorities stopped and searched a Syria-bound cargo plane from Iran for weapons on October 28, after carrying out a similar inspection on October 2.
Both planes were allowed continue their journey on to Syria when their cargo was cleared.
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The United States has been pressing Baghdad to ensure all Iranian aircraft flying through its airspace are ordered to land and checked for weapons, but Iraq has said it will only stop planes when it has doubts about the cargo.
"In the two cases which our planes were inspected by Iraq it showed that such claims are lies," Mehmanparast said.
Mehmanparast added that "Western accusations against Iran are to show that the instability in Syria is not due to their support and supply of weapons to terrorist groups."
Tehran, a staunch backer of Syrian President Bashar al-Assad, has been accused of arming his regime, but maintains it is only offering humanitarian aid.
Iraq has pointedly avoided calling for the departure of Assad, whose forces are locked in a 19-month conflict with rebels who are trying to overthrow his regime.