"The operation's target is not against a country or a person but against terrorist organisations only," Erdogan told local neighbourhood chiefs in Ankara.
"No one should have any doubts or take our statements to mean something else. Even if Turkey is left alone, it will continue its fight against terrorist organisations."
Turkey launched its unprecedented operation in northern Syria in August, providing tanks and aerial support to opposition fighters as they retake territory from the Daesh group.
Erdogan had on Tuesday said Turkey launched the offensive to "put an end to the rule of the tyrant Assad who carries out state terror, not for anything else".
The next day, Assad's close ally Moscow which is providing key military support to Damascus, demanded an explanation.
Kremlin spokesman Dmitry Peskov said Erdogan's comments did not reflect his previous remarks nor Russia's "understanding of the situation".
The Syrian foreign ministry also denounced the comments, saying they showed "clearly that the flagrant Turkish aggression against the Syrian territory is only the result of the ambitions and the illusions of an extremist despot".
Erdogan and Russian President Vladimir Putin discussed Syria three times on the phone this week including on Wednesday night. No mention has been made by either side over whether they discussed Erdogan's remarks.