"As our jet fighters were carrying out a mission against hotbeds of the ISIL terrorist group in Syria's Raqqa city, one of our warplanes crashed and its pilot taken hostage by ISIL," the army said in a statement, quoting an unnamed military source.
"Jordan holds the ISIL and its supporters responsible for the pilot's safety," it added.
The ISIL had said earlier that its fighters had shot down a military jet and captured Jordanian pilot Moaz al-Kasasba in Raqqa.
Photos of the captured pilot were shared on social media by pro-ISIL users, although their authenticity could not be independently verified.
The photos show a pilot apparently in good health.
ISIL-held Raqqa has been targeted several times by an international anti-ISIL coalition led by the U.S.
Over the summer, the militant group captured large swathes of land in Iraq and Syria, declaring the captured territories an "Islamic caliphate" and killing thousands of people – and displacing millions more – in the process.
The U.S. is leading an international coalition that has carried out numerous airstrikes against ISIL targets in Iraq and Syria since the militant group captured the northern Iraqi city of Mosul in June.