Russia launched a second air strike on U.S.-backed Syrian fighters battling Islamic State, even after the U.S. military used emergency channels to ask Moscow to stop after the first strike, a U.S. official told Reuters on Friday.

The official, who spoke to on condition of anonymity, said a small number of Syrian fighters were killed in Thursday's air strikes in southern Syria.

The Pentagon has criticized the strike near al-Tanf, saying it raised concerns about Russian intentions in Syria and promising to bring up the matter with Russia. No Russia or Russian-backed Syrian ground forces were in the area at the time.

"This was an attack on forces first of all that were fighting ISIL. And obviously that's the first thing that's problematic about this Russian conduct," U.S. Defense Secretary Ash Carter told reporters, using an acronym for the radical group Islamic State.

"The Russians initially said they were coming in to fight ISIL, and that's not what they did."

Asked about the incident, the Kremlin said on Friday it was hard to distinguish between moderate and Islamist extremist rebels on the ground when it came to targeting air strikes in Syria because they were frequently fighting close to one another.