The program did have periods of success, including in 2015 when rebels using tank-destroying missiles, supplied by the C.I.A. and also Saudi Arabia, routed government forces in northern Syria. But by late 2015 the Russian military offensive in Syria was focusing squarely on the C.I.A.-backed fighters battling Syrian government troops. Many of the fighters were killed, and the fortunes of the rebel army reversed.
Charles Lister, a Syria expert at the Middle East Institute, said he was not surprised that the Trump administration ended the program, which armed and trained thousands of Syrian rebels. (By comparison, a $500 million Pentagon program that envisioned training and equipping 15,000 Syrian rebels over three years, was canceled in 2015 after producing only a few dozen fighters.)
“In many ways, I would put the blame on the Obama administration,” Mr. Lister said of the C.I.A. program. “They never gave it the necessary resources or space to determine the dynamics of the battlefield. They were drip-feeding opposition groups just enough to survive but never enough to become dominant actors.”
Mr. Trump has twice publicly criticized the effort since he ended it. AfterThe Washington Post first reported on his decision, Mr. Trump tweeted that he was ending “massive, dangerous, and wasteful payments to Syrian rebels fighting Assad.” During an interview with The Wall Street Journal last month, the president said many of the C.I.A.-supplied weapons ended up in the hands of “Al Qaeda” — presumably a reference to the Qaeda-affiliated Nusra Front, which often fought alongside the C.I.A.-backed rebels.
Michael V. Hayden, a former C.I.A. director, said the president’s comments “might give the agency pause with regard to how much he will have their backs on any future covert actions.”
Gen. Raymond A. Thomas III, the commander of United States Special Operations Command, said during a conference last month that ending the C.I.A. program was a “tough, tough decision.”
“At least from what I know about that program and the decision to end it, it was absolutely not a sop to the Russians,” he said. “It was, I think, based on an assessment of the nature of the program, what we’re trying to accomplish, the viability of it going forward.”
A C.I.A. spokesman declined to comment.
President Barack Obama had reluctantly agreed to the program in 2013 as the administration was struggling to blunt the momentum of Syrian government forces loyal to President Bashar al-Assad. It soon fell victim to the constantly shifting alliances in Syria’s six-year-old civil war and the limited visibility that American military and intelligence officials had over what was occurring on the ground.
Once C.I.A.-trained fighters crossed into Syria, C.I.A. officers had difficulty controlling them. The fact that some of their C.I.A. weapons ended up with Nusra Front fighters — and that some of the rebels joined the group — confirmed the fears of many in the Obama administration when the program began. Although the Nusra Front was widely seen as an effective fighting force against Mr. Assad’s troops, its Qaeda affiliation made it impossible for the Obama administration to provide direct support for the group.
American intelligence officials estimate that the Nusra Front now has as many as 20,000 fighters in Syria, making it Al Qaeda’s largest affiliate. Unlike other Qaeda affiliates such as Al Qaeda in the Arabian Peninsula, the Nusra Front has long focused on battling the Syrian government rather than plotting terrorist attacks against the United States and Europe.
The American officials spoke on the condition of anonymity because they did not want to be identified discussing a program that is classified.
In the summer of 2012, David H. Petraeus, who was then C.I.A. director, first proposed a covert program of arming and training rebels as Syrian government forces bore down on them.
The proposal forced a debate inside the Obama administration, with some of Mr. Obama’s top aides arguing that Syria’s chaotic battlefield would make it nearly impossible to ensure that weapons provided by the C.I.A. could be kept out of the hands of militant groups like the Nusra Front. Mr. Obama rejected the plan.
But he changed his mind the following year, signing a presidential finding authorizing the C.I.A. to covertly arm and train small groups of rebels at bases in Jordan. The president’s reversal came in part because of intense lobbying by foreign leaders, including King Abdullah II of Jordan and Prime Minister Benjamin Netanyahu of Israel, who argued that the United States should take a more active role in trying to end the conflict.
Given the code name Timber Sycamore, the covert program began slowly, but by 2015 the C.I.A.-backed rebel groups had made significant progress against Syrian forces, pushing into areas of the country long considered to be government strongholds. The offensive gained momentum after the C.I.A. and Saudi Arabia began supplying the powerful tank-destroying weapons to the rebel groups.
But the rebel push in Idlib, Hama and Latakia Provinces in northern Syria also created problems for Washington. The Nusra Front, often battling alongside the C.I.A.-supported rebel groups, made its own territorial gains.
It was Nusra’s battlefield successes that Mr. Putin used as one justification for the Russian military offensive in Syria, which began in 2015. The Russian campaign, a relentless bombing of the C.I.A.-backed fighters and Nusra militants, battered the rebels and sent them into retreat.
The program suffered other setbacks. The arming and the training of the rebels occurred in Jordan and Turkey, and at one point Jordanian intelligence officers pilfered stockpiles of weapons the C.I.A. had shipped into the country for the Syrian rebels, selling them on the black market. In November, a member of the Jordanian military shot and killed three American soldiers who had been training Syrian rebels as part of the C.I.A. program.
White House officials also received periodic reports that the C.I.A.-trained rebels had summarily executed prisoners and committed other violations of the rules of armed conflict. Sometimes the reports led to the C.I.A. suspending cooperation with groups accused of wrongdoing.
John O. Brennan, Mr. Obama’s last C.I.A. director, remained a vigorous defender of the program despite divisions inside the spy agency about the effort’s effectiveness. But by the final year of the Obama administration, the program had lost many supporters in the White House — especially after the administration’s top priority in Syria became battling the Islamic State, also known as ISIS or ISIL, rather than seeking an end to Mr. Assad’s government.
During one meeting in the White House Situation Room at the end of the Obama administration, with C.I.A.-backed rebels continuing to lose ground in the face of withering Russian air bombing, Mr. Brennan pressed the case that the United States continue to back the effort to topple Mr. Assad, according to one person who attended the meeting.
But Susan E. Rice, the national security adviser, shot back. “Make no mistake,” she said, according to the person in the meeting. “The president’s priority in Syria is fighting ISIS.”
Backed by Russian aircraft, Syrian government forces gradually began to reclaim areas near the Turkish border that had long been rebel strongholds, and eventually pushed many of the rebels back to the besieged city of Aleppo.
Aleppo fell to Syrian government troops in December.