Russian and American warplanes confronted one another in the skies above Syria after Moscow bombed an elite force of US-trained rebels.

The Pentagon on Friday scrambled F/A-18 fighters to fend off an attack by Moscow's most advanced bombers on moderate opposition fighters it is supporting.

When the F/A-18s approached the Russians moved out of the area, but when the US fighters paused to refuel they returned and struck the base again, in what appeared to be a deliberately provocative move.

The Russians had been ordered to back off by the US pilots directly using a special communications channel set up to prevent air accidents, but were ignored.

Shortly after, US military officials held a video conference with Russia in which they "expressed strong concerns about the attack on the coalition-supported counter-Isil forces at the Al-Tanf garrison, which included New Syrian Army forces that are participants in the cessation of hostilities in Syria," said Pentagon spokesman Peter Cook.

The Russians claimed on Sunday that the location given by the US did not match what was on the ground.

"The Russian side explained that the target that was bombed is 300 kilometres from the area identified by the Americans as the location of Syrian opposition groups participating in the ceasefire," said Major General Igor Konashenkov, a Russian military spokesman, commenting on talks with the US after the incident.