Bashir was invited to attend a ceremony in Tehran for the inauguration of President Hassan Rouhani. The Saudi government closed its airspace Sunday to the Sudanese president's plane as it prepared to travel to the ceremony.
"We were informed by the Sudanese Embassy in Tehran that one of the countries on the flight route of Omar al-Bashir's plane did not give the permission for his plane to fly over its airspace," government spokesman Abbas Araqchi was quoted as saying by the semiofficial Fars News Agency. "If it is true that this country has committed such an act, it is deeply regrettable."
Saudi Arabia, a Sunni-led kingdom, and Iran, led by a Shiite administration, are long time foes.
The International Criminal Court called for the immediate arrest of Bashir last month. He left an HIV conference hosted by the African Union in Nigeria following calls for his arrest.
The ICC said Bashir is wanted for five counts of crimes against humanity and two counts of war crimes for atrocities allegedly committed during the Darfur genocide, which began in 2003.
Iran signed the treaty creating the ICC in 2000.
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