AMMAN, Jordan — Weapons shipped into Jordan by the Central Intelligence Agency 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 American and Jordanian officials.
Some of the stolen weapons were used in a shooting in November that killed two Americans and three others at a police training facility in Amman, F.B.I. officials believe after months of investigating the attack, according to people familiar with the investigation.
The existence of the weapons theft, which ended only months ago after complaints by the American 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 C.I.A. 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.
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 arms 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. Weapons smugglers also buy weapons in the arms bazaars to ship outside the country.
The F.B.I. investigation into the Amman shooting, run by the bureau’s Washington field office, is continuing. But American and Jordanian officials said the investigators believed that the weapons a Jordanian police captain, Anwar Abu Zaid, used to gun down two American contractors, two Jordanians and one South African had 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 H. 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 powerful Jordanian intelligence service, known as the General Intelligence Directorate, or G.I.D., “a world-class, reputable institution known for its professional conduct and high degree of cooperation among security agencies.” In Jordan, the head of the G.I.D. is considered the second most important man after the king.
Representatives of the C.I.A. and F.B.I. declined to comment.
The State Department did not address the allegations directly, but a spokesman said America’s relationship with Jordan remained solid.
“The United States deeply values the long history of cooperation and friendship with Jordan,” said John Kirby, the spokesman. “We are committed to the security of Jordan and to partnering closely with Jordan to meet common security challenges.”
The training program, which in 2013 began directly arming the rebels under the code name Timber Sycamore, is run by the C.I.A. and several Arab intelligence services and aimed at building up forces opposing President Bashar al-Assad of Syria. The United States and Saudi Arabia are the biggest contributors, with the Saudis contributing both weapons and large sums of money, and with C.I.A. paramilitary operatives taking the lead in training the rebels to use Kalashnikovs, mortars, antitank guided missiles and other weapons.