Asked about the reports, Mohammad Ali Hosseini, Iranian foreign ministry spokesman, implied al-Maliki's jet may have faced an issue over permission to fly across Iran but said it was not an unusual problem.
"Permission for Maliki's flight is a normal issue. All flights need permission," he told a weekly news conference in Tehran, without giving further details.
Al-Maliki, a Shia, visited Tehran last September to urge Iran not to interfere in Iraq.
Washington accuses Iran of stoking violence in Iraq and in January detained five men it says were linked to Iran's Revolutionary Guards and who were backing fighters in the country.
Iran insists the men are diplomats and has asked for their release.
Hoshiyar Zebari, Iraq's foreign minister, said last week that the Iraqi government was trying to secure the release of the five Iranians, who were detained by US forces during a raid on an Iranian government office in the northern Iraqi city of Arbil on January 11.
An Iranian diplomat freed two months after being kidnapped in Baghdad by gunmen wearing Iraqi army uniforms said on Saturday that he was tortured by US forces while in captivity.
Iran has previously blamed the US military for his abduction but US officials have denied any role.