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This is the first US-led coalition aircraft to be lost on IS territory since air strikes began in September.
Jordan is one of four Arab states which have bombed targets in Syria.
The confirmation that a Jordanian pilot had been captured came in a statement carried by the state news agency, Petra
"During a mission Wednesday morning conducted by several Royal Jordanian Air Force planes against hideouts of the IS terrorist organisation in the Raqqa region, one of the planes went down and the pilot was taken hostage," a military source was quoted as saying.
"Jordan holds the group and its supporters responsible for the safety of the pilot and his life," the source added.
Jordan's government spokesman Mohammad Al-Momani told satellite TV station Al Hadath the jet fighter "was shot at from the ground by rocket missiles and was brought down" and that an attempt to rescue the pilot before he was captured failed. He did not elaborate.