"We regret that we have yet to completely neutralise their offensive," Kremlin spokesman Dmitry Peskov said of the fighters return to the fabled city after an eight-month absence.
"We also regret that there still is a lack of coordinated action and real cooperation with other states -- with the United States first and foremost -- that do not want to cooperate, and this cooperation could allow us to avoid such attacks by terrorists."
Peskov added that jihadists from neighbouring Iraq, where a Western coalition is supporting the Iraqi military's efforts to retake the city of Mosul from IS, had been flooding into Syria.
Russia has carried out a bombing campaign in Syria in support of its long-standing President Bashar al-Assad since September 2015.
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Syrian troops backed by Russian air strikes and special forces on the ground recaptured the UNESCO world heritage site from IS fighters in March, delivering a major propaganda coup for both Damascus and Moscow.
Regime forces are currently focused on a major offensive fighting other insurgent groups in the second city of Aleppo that has seen them seize back most of the rebel-held stronghold.