"Evidence clearly indicates that ISIL did not down the aircraft as the terrorist organization is claiming," said US Central Command, the body overseeing the coalition air war over Iraq and Syria.
The statement did not give a cause for the "crash," and confirmed the lost jet's Jordanian pilot had been taken captive by IS guerrillas.
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"We strongly condemn the actions of ISIL, which has taken captive the downed pilot," said CentCom commander General Lloyd Austin.
"We will support efforts to ensure his safe recovery, and will not tolerate ISIL's attempts to misrepresent or exploit this unfortunate aircraft crash for their own purposes."
"The Jordanians are highly respected and valued partners and their pilots and crews have performed exceptionally well over the course of this campaign," he added.