At least 90 Syrian soldiers were said to have been killed in the airstrike on Saturday.
The Russian Defence Ministry said on Saturday that U.S. jets had killed more than 60 Syrian soldiers in the eastern Syrian city of Deir al-Zor in four air strikes by two F-16s and two A-10s coming from the direction of Iraq.
The Syrian Observatory for Human Rights, a Britain-based monitoring group with contacts across Syria, cited a military source at Deir al-Zor airport as saying at least 90 Syrian soldiers had been killed.
Russia's Foreign Ministry said in a strongly worded statement that the United States' position on the incident was "unconstructive and inarticulate".
"The actions of coalition pilots - if they, as we hope, were not taken on an order from Washington - are on the boundary between criminal negligence and connivance with Islamic State terrorists," the ministry said.
"We strongly urge Washington to exert the needed pressure on the illegal armed groups under its patronage to implement the ceasefire plan unconditionally. Otherwise the implementation of the entire package of the U.S.-Russian accords reached in Geneva on Sept. 9 may be jeopardized."
Russia has repeatedly called on the United States to push units of moderate Syrian opposition to separate from Islamic State and other "terrorist groups".
The Foreign Ministry said Saturday's incident was a result of Washington's "stubborn refusal" to cooperate with Moscow in fighting Islamic State, the Nusra Front - now renamed Jabhat Fatah al Sham - and "other terrorist groups".
The U.S. military said the coalition stopped the attacks against what it had believed to be Islamic State positions in northeast Syria after Russia informed it that Syrian military personnel and vehicles may have been hit.
Washington further unnerved Moscow when its envoy to the United Nations abruptly left her seat as the Russian representative took the floor to condemn the air strikes at an emergency U.S. Security Council meeting.
"We are reaching a really terrifying conclusion for the whole world: That the White House is defending Islamic State. Now there can be no doubts about that," Russian Foreign Ministry spokeswoman Maria Zakharova said in comments aired by state TV.
The U.S. ambassador to the United Nations, Samantha Power, said Zakharova should be embarrassed by that claim. Russia's U.N. representative Vitaly Churkin said Russia had no "specific evidence" of the U.S. colluding with Islamic State militants.
The diplomatic row is likely to further complicate the delivery of humanitarian aid to Syria, including its largest pre-war city of Aleppo where the situation remains especially tense and Monday's fragile truce has been repeatedly violated.
The U.N. told Reuters aid trucks that had been expected to move to Aleppo on Sunday morning were once again being delayed.
"It's a tough moment," one top aid official in Geneva told Reuters. "The U.N. convoys are highly politicised."