In a statement the Russian military said it had received reports from Syrian generals that regime forces that crossed the strategic Euphrates River were faced with "gunfire from the north" near Deir Ezzor.
Moscow claimed that shooting came from a zone controlled by the Syrian Democratic Forces (SDF) supported by Washington.
The statement also accused the rebels of opening dams on the Euphrates to stop government forces from crossing the river.
"A few hours after the Syrian forces started to cross the river, the water level rose and the speed of outflow doubled," it said.
Despite this, Russia said that Syrian forces have captured some 60 square kilometres (23 square miles) of territory on the eastern side of the river after bridging it on Monday.
Until Monday, Syrian troops had been fighting only west of the Euphrates, while the US-backed Syrian Democratic Forces waged a rival offensive against IS east of the river.
To prevent the two operations from clashing, the coalition, the SDF, Syria's government and Russia have agreed on a "de-confliction line" in northeast Syria.
That line runs from the neighbouring province of Raqa southeast along the Euphrates to Deir Ezzor.
On Saturday, however, the US-led coalition backing the SDF accused Russian aviation of bombing them in the north east of Deir Ezzor, which Moscow denies.
A spokesman for the US-led coalition targeting IS Colonel Ryan Dillon said he did not "know how that could be the case" that the SDF or coalition were slowing the Syrian advance.
Dillon said it was "beneficial" to have all sides there, adding: "IS now has to swivel their heads to the east and to the west and to the north, because they're being assaulted from so many different directions".
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