In a statement that was published by the website of the Jordanian army, the general added that early indications had showed that the plane was not shot down by ISIL, which controls the Syrian city.
Nevertheless, the general went on to say that it was difficult to determine the reason why the plane fell down.
He said the Jordanian army could not reach either the debris of the plane, or its pilot, who was taken hostage by ISIL.
On Wednesday, ISIL claimed that it had shot down a Jordanian air force plane that launched strikes against the targets of the militant movement in the Syrian city.
Jordan is one of several countries participating in a United States-led coalition that has been striking ISIL – from air so far – both in Iraq and Syria, where it has captured large swaths of land.
The militant movement, which contains thousands of foreign fighters, published photos of some of its fighters boastfully arresting the Jordanian pilot of the plane .
The Pentagon said in a statement on Wednesday that there were indications that ISIL did not down the aircraft.