The Syrian Observatory for Human Rights, cited a military source at Deir al-Zor airport as saying that at least 80 Syrian soldiers had been killed in the strike.
The U.S. military, in an apparent admission that it may have hit the position, said in a statement that coalition air strikes near Deir al-Zor had been halted when Russia told coalition officials they may have hit the Syrian army.
Syria's army general command said in a statement that the air strike was "conclusive evidence" of U.S. support for Islamic State, noting that the strike was "dangerous and blatant aggression".
Islamic State said in a statement on its Amaq news channel that it had gained "complete control" over Jebel Tharda but both Syrian state television and Russian state media said the positions lost to the militant group were later recaptured.
The defence ministry in Russia, which has been aiding Syria's President Bashar al-Assad in the civil war, said U.S. jets had killed more than 60 Syrian soldiers in four air strikes by two F-16s and two A-10s coming from the direction of Iraq.
"Syria is a complex situation with various military forces and militias in close proximity, but coalition forces would not intentionally strike a known Syrian military unit," U.S. officials said.
The Syrian Observatory for Human Rights, a Britain-based monitoring group with contacts across the country, cited a military source at Deir al-Zor airport as saying that at least 80 Syrian soldiers had been killed in the strike.
Russia's Defence Ministry said that if the coalition bombing was a mistake, it was evidence of Washington's "stubborn refusal" to coordinate its actions with Russia's government.
The U.S.-led coalition has been conducting air strikes against Islamic State since September 2014 and is also supporting rebels against Assad elsewhere in Syria.
The Observatory said that Russian jets had been conducting bombing in the area at the same time, and that violent clashes took place afterwards between Islamic State and the Syrian army around the position.
Syria's army controls Deir al-Zor airport and parts of the city which are otherwise entirely surrounded by territory held by Islamic State.
The United States and Russia agreed a deal on Syria last week, involving a ceasefire which came into effect on Monday, aid deliveries to besieged areas and eventual joint targeting of militant jihadist groups if the truce works out.
Syria's war between Assad and rebels seeking to topple him has drawn in regional and global powers and allowed militant jihadist groups including Islamic State to gain territory and inspire attacks.