US-led warplanes on Thursday carried out a strike in the east of the country against a convoy of pro-government forces.
"Any military actions that lead to a deterioration in the situation in Syria obviously impact the political process," deputy foreign minister Gennady Gatilov was quoted as saying by state-run RIA Novosti in Geneva.
"Such actions that were carried out against the Syrian armed forces... this is completely unacceptable, this is a breach of Syrian sovereignty," he said.
US-led warplanes on Thursday carried out a strike in the east of the country against a convoy of pro-government forces headed towards a remote coalition garrison near the border with Jordan.
In a statement, the US-led coalition said it had struck "pro-regime forces... that posed a threat to US and partner forces."
The coalition said the strike came after unsuccessful "Russian attempts to dissuade Syrian pro-regime movement" as well as "a coalition aircraft show of force, and the firing of warning shots."
Russia and Iran have deployed forces to Syria to back up leader Bashar al-Assad while the US and many of its regional and Western allies have called for the strongman to leave power.
The United States in April infuriated the Kremlin by bombing a Syrian regime airbase in response to an alleged chemical attack by Damascus.
Representatives of Syria's government and opposition High Negotiations Committee are in Switzerland for the sixth round of UN-backed peace negotiations, but there has been little sign of progress.
In the first concrete results from talks this week on ending Syria's conflict, the United Nations said the warring sides had agreed to set up expert committees to discuss "constitutional issues."
Another deputy foreign minister, Mikhail Bogdanov, told TASS news agency that Russia "supports" the move.