The Russian Ministry of Defence said the US-backed Syrian Democratic Forces have already shelled Syrian government positions outside of Deir el-Zour twice in recent days.
The Russian special forces deployment raises the specter of a direct confrontation on the ground between Russian forces and pro-Syrian troops they back on one side, and the US- supported Kurdish-led Syrian forces on the other.
"Syrian forces have twice come under massive mortar and rocket artillery fire coming from the areas on the eastern bank of the Euphrates where SDF fighters and US special forces are deployed," Russian Defence Ministry spokesman Maj Gen Igor Konashenkov said in a statement.
Konashenkov said the warning was delivered to the US military command. Russian special forces have been deployed to help Syrian government forces fighting the IS militants outside Deir el-Zour, he also said today.
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"Attempts to open fire from SDF-controlled areas would be immediately met with retaliation," he said. "The firing positions in those areas will be immediately destroyed with all the arsenal at our disposal."
The SDF has already accused Russia of targeting its troops in Deir el-Zour in an airstrike last week, a claim Moscow denied.
Russia began its operation to support President Bashar Assad's offensive against the IS in Syria in 2015 but has mostly focused on providing air cover to government troops on the ground.
The campaign in Deir el-Zour, Syria's oil-rich eastern province, is caught up in a race between the Russian-backed government troops and the US-backed Syrian Democratic Forces.
The Russian-backed campaign has so far been to recapture the city and provincial capital, also called Deir el-Zour.
The US-backed offensive is focused on the Iraq border area, which is still controlled by IS. Washington fears that further advances by pro-government forces could help Iran, which also has thousands of militiamen fighting alongside the Syrian government, expand its influence across the region via a land bridge spanning through Iraq, Syria and Lebanon, all the way to Israel.