Over the past week, Russia has directed parts of its air campaign against US-funded groups and other moderate opposition in a concerted effort to weaken them, the officials say.
The Obama administration has few options to defend those it had secretly armed and trained.
The Russians "know their targets, and they have a sophisticated capacity to understand the battlefield situation," said Republican Rep Mike Pompeo, who serves on the House Intelligence Committee and was careful not to confirm a classified program.
Other US officials interviewed spoke on condition of anonymity because they were not authorized to discuss the matter publicly.
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The CIA began a covert operation in 2013 to arm, fund and train a moderate opposition to Assad. Over that time, the CIA has trained an estimated 10,000 fighters, although its current size isn't clear.
The effort was separate from the one run by the military, which trained militants willing to promise to take on IS exclusively.
That program was widely considered a failure, and on Friday, the Defense Department announced it was abandoning the goal of a US-trained Syrian force, instead opting to equip established groups to fight IS.
Some CIA-supported rebels had been captured; others had defected to extremist groups. The secret CIA program is the only way the U.S. Is taking on Assad militarily. In public, the United States has focused its efforts on fighting IS and urging Assad to leave office voluntarily.
"Probably 60 to 80 percent of the arms that America shoveled in have gone to al-Qaeda and its affiliates," said Joshua Landis, a Syria expert at the University of Oklahoma.
But in recent months, CIA-backed groups, fighting alongside more extremist factions, began to make progress in Syria's south and northwest, American officials say. In July and August, US-supported rebels seized territory on the al-Ghab plain, in northwest Syria's Idlib and Hama governorates.