The US-backed Syrian Democratic Forces - an alliance of Kurdish and Arab fighters - is battling to oust the militants from Raqqa, and broke into the IS stronghold city last week.
Updated at 8:51 a.m.
On June 18, a United States fighter jet from the worldwide coalition shot down a Su-22 fighter of the Syrian Air Force using an air-to-air missile.
An escalation? The US downed a Syrian fighter in order to protect rebel forces.
"Any aircraft, including planes and drones of the global coalition, detected in the operation areas west of the Euphrates River by the Russian air forces will be followed by Russian ground-based air defense and air defense aircraft as air targets", the ministry said.
The U.S. shot down the Syrian regime aircraft Sunday after repeated warnings to stop engaging U.S. -backed anti-ISIS fighters.
Russian Federation has been a staunch supporter of Syria's beleaguered President Bashar Assad and has been providing an air cover for his offensive against IS since 2015.
USA officials say the aircraft had struck America's rebel allies. Defence Minister Sergei Shoigu later said that the mechanism to avert conflict in the skies between Russian and US-led forces continues to operate despite a formal end to the pact.
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The Syrian plane was shot down by a U.S. Navy fighter jet after attempting to bomb U.S. -allied coalition forces, according to the U.S. military.
The top US military officer said Monday that Washington and Moscow are in delicate discussions to tamp down tensions arising from the USA shootdown of a Syrian fighter jet, which the Russians called a violation of a U.S.
"The Coalition does not seek to fight Syrian regime, Russian, or pro-regime forces partnered with them, but will not hesitate to defend Coalition or partner forces from any threat", it said. Coalition aircraft stopped the pro-regime forces from advancing on Ja'Din.
Government forces have also been attacking IS in northern, central and southern Syria, seizing 25,000 square kilometers (9,600 square miles) and reaching the Iraqi border for the first time in years.
Both Russia and the U.S. are engaged in military action Islamic State targets in Syria.
"The demonstrated hostile intent and actions of pro-regime forces toward coalition and partner forces in Syria conducting legitimate counter-ISIS operations will not be tolerated", it said.
US forces tangled earlier this month with Syria-allied aircraft in the region.