The Kremlin on Wednesday demanded an explanation after Turkish President Recep Tayyip Erdogan said Ankara intervened in Syria solely to topple President Bashar al-Assad.
Turkish forces are pressing on with a three month operation inside war-torn Syria in support of anti-Assad forces, while Russia is the chief ally of the Syrian president in the conflict that has claimed more than 300,000 lives since 2011.
Yet Turkey and Russia have also been working hard to improve relations after clinching a reconciliation deal in June to repair ties brought to a historic low by Turkey's shooting down of a Russian jet in November 2015.
Erdogan had said Tuesday at a meeting in Istanbul in support of the Palestinians: "We went in there to put an end to the rule of the tyrant Assad who carries out state terror, not for anything else."
His comments came as Russian Foreign Minister Sergei Lavrov is due to meet Turkish counterpart Mevlut Cavusoglu for talks in the Turkish resort of Alanya on Thursday.
Kremlin spokesman Dmitry Peskov told journalists he hoped that "clarification will come shortly from our Turkish partners".
Peskov said Erdogan's comment "really came as news," adding that it "is not in harmony with previous statements" and "not in harmony with our understanding of the situation".
Turkey is waging the operation inside Syria against Islamic State (IS) militants and also Kurdish militia to back pro-Ankara rebels, in an unprecedented military incursion.
There has so far been no indication of clashes with Assad's forces in the operation or that Turkey plans any offensive against regime-held territory.
Russia has generally steered clear of any sharp criticism of the Turkish offensive.
But the Turkish army accused the Syrian regime last week of launching an airstrike that killed four Turkish soldiers in Syria, the first time it has made such a claim during the incursion.
Erdogan has repeatedly pushed for the ouster of Assad as the only solution to end the Syrian civil war and had, until recently, vehemently criticised Russia's military support for his forces and even accused President Vladimir Putin of "war crimes".
But since the deal to normalise ties between Turkey and Russia, Ankara has been remarkably muted in its criticism of Russia's actions -- in particular its backing for Assad forces in the battle for Aleppo.
Erdogan and Putin discussed the Syria conflict on Saturday by telephone for the second time in just over 24 hours.