Weapons from the Central Intelligence Agency and Saudi Arabia intended for a Syrian rebel training program were stolen by Jordanian intelligence agents and sold on the black market, U.S. and Jordanian officials said in a joint investigation by Al Jazeera and The New York Times, which raises questions about a trend in which CIA operations tend to do more harm than good in the region.

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The officials said some of the stolen weapons were used in a shooting in November in which a Jordanian officer shot dead two U.S. security contractors, a South African trainer and two Jordanians at a U.S.-funded police training facility near Amman before being killed in a shootout.

Authorities cracked down on the theft of weapons and supplies, which is believed to have happened more than once, amid pressure from Saudi Arabia and the U.S. on Amman to act against the corrupt agents, the investigation claimed.

Jordanian officers who were part of the plan “reaped a windfall” from the sale of weapons, making millions of dollars and using the money to buy iPhones, SUVs and other luxury items, Jordanian officials told the newspaper.

While some of the weaponry has been sold to tribes in rural Jordan and other criminal networks in the country, the location of most of the kitty remains unknown and has possibly been shipped out of the country, most likely to armed groups in neighboring Syria.

The recent revelations expose how the CIA and other powerful governments in the region such as Saudi Arabia continue to interfere in the Syrian conflict and push for their own agenda through questionable means.

The CIA’s weapons delivery to “favorable” and moderate rebels in Syria brings back memories of when the agency provided the same support to Afghanistan's Mujahideen groups, within which Osama bin Laden was a prominent participant, through Pakistani intelligence in order to fight Soviet forces in the country in the midst of the Cold War.

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Arab participants within the Mujahideen, including Bin Laden went on to establish al-Qaida, one of the most dangerous extremist groups in the world whose main enemy is the United States and its allies.

However, Jordanian Minister of State for Media Affairs Mohammad al-Momani said allegations that Jordanian intelligence officers had been involved in the theft of any weapons was "absolutely incorrect."

"Weapons of our security institutions are concretely tracked, with the highest discipline," he said.

He called the powerful Jordanian intelligence service known as the General Intelligence Directorate, or locally known as Mukhabarat, "a world-class, reputable institution known for its professional conduct and high degree of cooperation among security agencies."

The revelations are embarrassing for both Jordan and the United States. In Jordan the GID is considered the second most important institution after the throne and its head answers directly to the king.

To add to the embarassment, the GID was actually established using financial, technical and strategic support from the CIA.

According to Al Jazeera, the late King Hussein, who ruled Jordan from 1952 until his death in 1999, received large amounts of money from the CIA in exchange for permission to run numerous intelligence operations on Jordanian soil.

In return, the CIA and Washington helped him set up the GID, one of the strongest and most brutal spy agencies in the region, to help consolidate the monarchy's grip on power and squash external and internal threats.

Several reports by various human rights organizations claim the GID carries out systematic torture against dissented Jordanian citizens.