The US-backed Syrian Democratic Forces accuse Russian warplanes of bombing its fighters for the first time in eastern Syria.
The US-led coalition said on Saturday Russian forces bombed American-backed fighters battling IS in eastern Syria wounding several, despite denials from Syrian regime ally Moscow.
The unprecedented strike was initially reported by the Syrian Democratic Forces, an alliance of Kurdish and Arab fighters supported by Washington.
The SDF accused Russian warplanes of bombing its fighters for the first time in the complex war, but Russia's military spokesman denied targeting the group.
"This is not possible. Why would we bomb them?" military spokesman Igor Konashenkov told AFP at Hmeimim, Moscow's main base for its air operations in Syria.
A statement later by the coalition dismissed the Russian denial.
"Russian munitions impacted a location known to the Russians to contain Syrian Democratic Forces and coalition advisers. Several SDF fighters were wounded and received medical care as a result of the strike," the coalition statement said.
No coalition troops were wounded in the early morning strike east of the Euphrates River near Syria's oil-rich province of Deir Ezzor, the coalition added.
The SDF and Russian-backed Syrian government forces are conducting parallel but separate offensives against IS in Deir Ezzor.
Regime troops are engaged in an offensive against the provincial capital, Deir Ezzor city, while SDF fighters are battling the jihadists further east across the Euphrates.
The SDF earlier said six of its fighters were wounded in Russian and regime bombing of an industrial area northeast of the city, about seven kilometres (four miles) from the east bank of the Euphrates.
"At 3:30 am (0030 GMT) on September 16, 2017, our forces east of the Euphrates River were targeted by Russian and Syrian regime warplanes in the Al-Sinaaiya area," the SDF said.
The SDF's assaults against IS in Deir Ezzor and in Raqa further up the Euphrates Valley are both backed by the US-led coalition, while Syrian regime troops are supported by air cover from Russian warplanes.
The coalition says there is a de-confliction line to prevent the two offensives from clashing and that the line has been agreed between Russia, the regime, the SDF and the coalition.
The line runs from Raqa province southeast along the Euphrates River to Deir Ezzor.
The skies over Syria have become increasingly congested as the six-year conflict has dragged on, with warplanes from the coalition, the Syrian government and Russia all carrying out air strikes.
Confrontations between the warplanes have been rare, but in June a US fighter jet shot down a Syrian warplane accused of bombing SDF units in the north.
On Saturday, Britain-based monitor the Syrian Observatory for Human Rights said that IS had shot down a plane believed to belong to the regime southeast of Deir Ezzor.
Syrian presidential adviser Bouthaina Shaaban has said it is up to Russia and the United States to see that the SDF and the Syrian army do not clash.
Syria's crisis erupted with anti-government protests in 2011 but has since evolved into a complex, multi-front war that has killed 330,000 people and displaced millions.
IS, which in 2014 overran swathes of territory across Syria, is seeing its zones of control dwindle even as it claims responsibility for bloody attacks abroad.
It once held most of Deir Ezzor province and its capital, encircling around 100,000 civilians who still lived in government-controlled neighbourhoods there.
But Russian-backed troops breached the IS sieges on the city earlier this month and are now working to shut off the jihadists' remaining escape routes.
Pro-regime forces have also begun fighting to reach the IS-held town of Albukamal, according to a statement published by a joint operations room of loyalists including Iranian, Iraqi and Lebanese fighters from Hezbollah.
Albukamal lies on Syria's eastern border with Iraq and is regularly targeted by coalition air strikes.
IS has also been pushed out of two-thirds of its former bastion Raqa by the SDF.
Across the border in Iraqi desert territory, security forces backed by tribal fighters are manoeuvring to attack one of IS's last remaining bastions.
After driving IS out of Nineveh province earlier this year, the Iraqi government set its eyes on Hawija, north of Baghdad, as well as the towns of Al-Qaim, Rawa and Anna in the western desert.
On Saturday, Iraqi government forces captured the former mining town of Akashat some 100 kilometres (60 miles) south of Al-Qaim just hours after attacking the IS desert outpost.