Russia's defence ministry on Sunday denied bombing US-backed rebels in southern Syria earlier this week.

In a video conference with Russian military officials, the Pentagon said Saturday that it had expressed "strong concerns about the attack on the coalition-supported counter-ISIL forces at the Al-Tanaf garrison."

Hours later Russian defence ministry spokesman Igor Konashenkov denied that Russia had bombed areas where US-backed rebels are operating.

"The target that was bombed was located more than 300 kilometres away from the area" indicated by the United States, he said.

Konashenkov insisted that the Russian air force had acted "within the framework of the agreed procedures" and had given advance warning of its ground targets to the US-led coalition.

Russia's defence ministry said late Thursday that it had not carried out strikes against opposition forces included in the ceasefire but did not mention Al-Tanaf.

The Pentagon voiced its concerns as Russian Defence Minister Sergei Shoigu paid a surprise visit to Syrian President Bashar al-Assad in Damascus to discuss military cooperation "to fight against terrorist organisations on Syrian soil."

Konashenkov on Sunday also accused the United States of not providing the coordinates of the areas where the US-backed rebels are active, "not allowing for precision in the operations of the Russian air force."