Jordan's state television confirms a Jordanian Royal Air Force pilot has been captured by Islamic State militants in Syria during a mission. (Reuters)

A Jordanian pilot was captured by the Islamic State after his warplane crashed Wednesday while on a bombing run over Syria, the first such incident since a U.S.-led coalition began airstrikes against the militant group in the summer.

The militants claimed to have shot down the F-16 fighter with an antiaircraft missile, but a U.S. military statement said, without providing details, that “evidence clearly indicates” that was not the case.

“We can say with certainty that it was an aircraft crash and the plane was not downed by ISIL as was claimed by the terrorist organization,” said U.S. Navy Cmdr. Lisa Brackenbury, a Central Command spokeswoman, using an alternative acronym for the Islamic State. While “a thorough investigation will be conducted,” she said, “this was an aircraft crash and not the result of enemy action.”

Earlier, Jordanian Information Minister Mohammad Momani told the Associated Press that “it is our expectation that the plane went down because of fire from the ground, but it is difficult to confirm that.”

Both the United States and Jordan confirmed the capture of the pilot. The Islamic State posted images on social media sites of the man being pulled from a body of water and held by his neck while surrounded by masked militants.

The pilot, identified as Muath Safi al-Kaseasbeh, was seized near the Syrian city of Raqqa, the de facto capital of the Islamic State, after he apparently ejected from his aircraft.

The capture is a blow to the U.S.-led coalition and its Arab members — Bahrain, Jordan, Saudi Arabia and the United Arab Emirates — which began airstrikes against the Islamic State in Syria in September. Qatar also plays a logistical role in the coalition. The United States and European allies, including Britain, France and the Netherlands, are also striking the group in neighboring Iraq. U.S. and coalition aircraft fly long distances from bases in the Persian Gulf and aircraft carriers in the region, giving them little time to maneuver over strike areas.

“This happened early this morning, and our activists on the ground have confirmed that the pilot is still alive and being held near Raqqa,” said the head of the Britain-based Syrian Observatory for Human Rights, who goes by the pseudonym Rami Abdulrahman.

Gen. Lloyd J. Austin III, head of the Central Command, said in a statement that “the Jordanians are highly-respected and valued partners and their pilots and crews have performed exceptionally well over the course of this campaign. We strongly condemn the actions of ISIL which has taken captive the downed pilot. 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 pilot is the first known military member of a coalition force to be held by the Islamic State since the airstrikes began. Western civilian hostages have been exchanged for millions of dollars in ransom or, in the case of three Americans and two Britons, beheaded in videotaped executions.

Although the circumstances of the crash remain unclear, a shootdown could significantly change the risk assessment of air operations for coalition members, which have operated with impunity for months over Syria and Iraq.

In a statement issued Wednesday morning, the Central Command listed 10 airstrikes overnight in Syria — one of them said to have struck “an ISIL weapons stockpile” near Raqqa — and seven in Iraq and said that “all aircraft returned to base safely.” In a corrected version of the statement, issued moments later, that sentence had been removed.

The father of the Jordanian pilot captured by Islamic State asks his "Muslim brothers" to treat his son well. (Reuters)

U.S.-backed “moderate” rebels in Syria have long demanded that the United States supply them with portable surface-to-air missiles to combat Syrian President Bashar al-Assad’s air force. The United States has refused and has pressed regional allies such as Saudi Arabia not to supply those weapons on grounds that they could end up in the hands of militant groups such as the Islamic State.

But Islamic State fighters are thought to have purchased surface-to-air weapons systems on the black market or captured them from military bases they and other militant groups have overrun. Both Syria and Iraq have Russian-made missile systems in their arsenals.

In Iraq, Islamic State militants are thought to have used shoulder-fired missiles to down three Iraqi military helicopters in recent months. After a shootdown in October, the group released a video showing one of its fighters with a Chinese-made portable system.

Cunningham reported from Baghdad. Mustafa Salim in Baghdad and Karen DeYoung in Washington contributed to this report.