Ankara has been a prime foe of Assad throughout the conflict but has occasionally softened its rhetoric in the last months as Turkey strengthened cooperation with the regime's main ally Russia.
President Recep Tayyip Erdogan's spokesperson, Ibrahim Kalin, told journalists in Istanbul, that Assad was not the leader to unite Syria and had lost legitimacy.
But Kalin said there needed to be a "political transition in Syria", leading to a new constitution and elections.
"Where exactly, at what point precisely (Assad leaves), is something that will be answered as we go on, obviously," he said.
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Kalin was speaking after Russia on Tuesday hosted a peace congress on Syria, with both Russian President Vladimir Putin and Erdogan expressing "satisfaction", according to the Kremlin.
Kalin said the Russian position has been "not so much protecting Assad personally but protecting the state institutions, state apparatus and the Syrian army and the regime elements".
Turkey's position on Assad has been under ever greater scrutiny since Ankara on January 20 began a cross-border operation with Syrian allied rebel forces against Kurdish militia based in the town of Afrin.
But Kalin denied any contact with Damascus "at any level".
"There is no communication, no relationship, direct (or) indirect. Nothing with the Syrian regime, at any level. I can say that categorically and very clearly," he said.
He also rejected the notion that there had been any agreement with Russia allowing the Afrin operation to go ahead in exchange for a deal over the rebel-held neighbouring region of Idlib.