FBI officials believe some of the stolen weapons were used in a November shooting that killed two Americans and three others at a police training facility in Amman.

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AMMAN, Jordan — Weapons shipped to Jordan by the CIA and Saudi Arabia intended for Syrian rebels have been systematically stolen by Jordanian intelligence operatives and sold to arms merchants on the black market, according to U.S. and Jordanian officials.

FBI officials believe some of the stolen weapons were used in a November shooting that killed two Americans and three others at a police training facility in Amman, according to people familiar with the investigation.

The existence of the weapons theft, which ended only months ago after complaints by the U.S. and Saudi governments, is being reported for the first time after a joint investigation by The New York Times and Al-Jazeera. The theft, involving millions of dollars of weapons, highlights the messy, unplanned consequences of programs to arm and train rebels — the kind of program the CIA and Pentagon have conducted for decades — even after the Obama administration had hoped to keep the training program in Jordan under tight control.

The Jordanian officers who were part of the scheme reaped a windfall from the weapons sales, using the money to buy expensive SUVs, iPhones and other luxury items, Jordanian officials said.

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The theft and resale of the arms — including Kalashnikov assault rifles, mortars and rocket-propelled grenades — have led to a flood of new weapons available on the black market. Investigators do not know what became of most of them, but a disparate collection of groups, including criminal networks and rural Jordanian tribes, use the arms bazaars to build their arsenals. Smugglers also buy weapons in those bazaars to ship outside the country.

The FBI investigation into the Amman shooting, run by the bureau’s Washington field office, is ongoing. But U.S. and Jordanian officials said investigators think that the weapons used to gun down two American contractors, two Jordanians and one South African by a Jordanian police captain named Anwar Abu Zaidhad originally arrived in Jordan intended for the Syrian rebel-training program.

The officials said this finding had come from tracing the serial numbers of the weapons.

Mohammad al-Momani, Jordan’s minister of state for media affairs, said allegations that Jordanian intelligence officers had been involved in any weapons thefts were “absolutely incorrect.”

“Weapons of our security institutions are concretely tracked, with the highest discipline,” he said. He called the Jordanian intelligence service, known as the General Intelligence Directorate, or GID, “a world-class, reputable institution known for its professional conduct and high degree of cooperation among security agencies.” In Jordan, the head of the GID is considered the second most important man after the king.

Representatives from the CIA and FBI declined to comment.

The State Department did not address the allegations directly, but a spokesman said that America’s relationship with Jordan remained solid.

“The United States deeply values the long history of cooperation and friendship with Jordan,” said John Kirby, a spokesman for the department. “We are committed to the security of Jordan and to partnering closely with Jordan to meet common security challenges.”

The training program, which began directly arming the rebels in 2013 under the code name Timber Sycamore, is run by the CIA and several Arab intelligence services and is aimed at building up forces opposing Syrian President Bashar Assad.

The United States and Saudi Arabia are the biggest contributors, with the Saudis contributing both weapons and large sums of money, while CIA paramilitary operatives take the lead in training the rebels to use Kalashnikovs, mortars, anti-tank guided missiles and other weapons.

The existence of the program is classified, as are all details about its budget. U.S. officials say that the CIA has trained thousands of rebels in the past three years, and that the fighters made substantial advances on the battlefield against Syrian government forces until Russian military forces — launched last year in support of Assad — compelled them to retreat.

The program is separate from one that the Pentagon set up to train rebels to combat Islamic State fighters, rather than those from the Syrian military. That program was shut down after it trained only a handful of Syrian rebels.

Jordanian and U.S. officials described the weapons theft and subsequent investigation on the condition of anonymity because the Syrian rebel training is classified in the United States and a government secret in Jordan.

News of the weapons theft and eventual crackdown has been circulating inside Jordan’s government for several months. Husam Abdallat, a senior aide to several of the country’s past prime ministers, said he had heard about the scheme from current Jordanian officials. The GID has some corrupt officers in its ranks, Abdallat said, but added that the institution as a whole is not corrupt. “The majority of its officers are patriotic and proud Jordanians who are the country’s first line of defense,” he said.

Jordanian officials who described the operation said it had been run by a group of GID logistics officers with direct access to the weapons once they reached Jordan. The officers regularly removed truckloads of weapons from the stocks before delivering the rest of the weapons to designated drop-off points.

Word that the weapons intended for the rebels were being bought and sold on the black market leaked into Jordan government circles last year, when arms dealers began bragging to their customers that they had large stocks of U.S.- and Saudi-provided weapons.

Jordanian intelligence operatives monitoring the arms market — operatives not involved in the weapons-diversion scheme — began sending reports to headquarters about a proliferation of weapons in the market and the boasts of the arms dealers.

After the Americans and Saudis complained about the theft, investigators at the GID arrested several dozen officers involved in the scheme, among them a lieutenant colonel running the operation. They were ultimately released from detention and fired from the service, but were allowed to keep their pensions and money they had gained from the scheme, according to Jordanian officials.