Russia, which support's Assad along with Iran, has called on Washington to press the moderate Syrian opposition to separate itself from Islamic State and other "terrorist groups."
Iran also condemned the U.S. military action. "Such moves indicate America supports terrorist groups in Syria," a foreign ministry spokesman said, according to Iranian news agencies.
In Venezuela, Syrian U.N. Ambassador Bashar Ja'afari said the U.S.-led coalition strikes were intended to sink the ceasefire.
French Foreign Minister Jean-Marc Ayrault said that despite the strikes on the Syrians, Syrian government forces were principally behind the truce violations.
The U.S. military said the coalition stopped the attacks against what it believed to be Islamic State positions in northeast Syria after Russia informed it that Syrian forces may have been hit.
"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 U.S. collusion with Islamic State.
The dispute should further complicate humanitarian aid deliveries to Syria, including its largest pre-war city Aleppo, where the fragile truce is under threat.
Aleppo was hit by air strikes for the first time since the truce began. Moscow said militants there were preparing for large-scale military actions against Syria's army.
HEAVY CLASHES
Heavy clashes continued on Sunday east of Damascus in the rebel-held Jobar suburb, the Observatory and a witness said.
The al-Rahman Legion, part of a Free Syrian Army rebel alliance, said its fighters had destroyed a government tank and killed soldiers after government forces tried to storm Jobar for the second time this week.
The Observatory said at least eight people died and many were seriously injured when helicopters dropped barrel bombs in a rebel-held part of the southern Syrian province of Daraa on Sunday.
Insurgents say they only reluctantly accepted the initial deal to relieve the humanitarian situation in besieged areas they control, and blamed Russia for undermining the ceasefire.
"The truce ... will not hold out," a senior rebel official in Aleppo said.
Rebels have also accused Russia of using the ceasefire to give the Syrian army and allied militias a chance to regroup and deploy forces.
ISLAMIC STATE
Islamic State is excluded from the truce. Separate U.S.-led, Damascus-led and Turkey-backed operations against the militants have continued.
One Turkish soldier and six Syrian rebels were wounded on Sunday in clashes with Islamic State near the Syrian border town of al-Rai as Turkey-backed Syrian rebels pushed south toward the IS-held town of al-Bab, Turkey's Dogan News agency reported.
Turkey hit Islamic State targets within Syria with warplanes, according to Dogan, the Observatory and a rebel commander.
On Sunday, Islamic State said it had shot down a warplane in Deir al-Zor with "anti-aircraft" guns, the same area as the coalition strikes hit the Syrian military on Saturday.
The Syrian military confirmed the loss of a warplane it said was carrying out an operation against rebels.
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