Salah Khashoggi, who holds dual U.S. -Saudi citizenship and had thus far been under a travel ban, departed Saudi Arabia on Wednesday.
Meanwhile, world leaders continue to urge the Saudi authorities to clarify the circumstances of the journalist's killing.
An independent United Nations investigator says Saudi journalist Jamal Khashoggi was the victim of an "extrajudicial execution" carried out by the Saudi state.
The shifting explanations indicate Saudi Arabia is scrambling for a way out of the crisis that has enveloped the world's largest oil exporter and a major USA ally in the Middle East.
News of the call appeared to calm growing speculation that Turkey was edging toward implicating the crown prince, whose ambitions for a modernized Saudi Arabia have been undermined by his penchant for making enemies at home and overseas.
Khashoggi entered the Saudi consulate in Turkey's Istanbul on October 2 to obtain documentation for his upcoming marriage, but he never left the place.
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Still, neither Trump nor Saudi Arabia has been willing to implicate Saudi leadership in the journalist's killing.
US President Donald Trump has stated that it will be up to the US Congress to decide what to do in response to the killing.
Turkish media have also published a security camera image allegedly showing a vehicle belonging to the Saudi Consulate "scouting" a forest in the outskirts of Istanbul before Khashoggi was killed.
Pro-government Turkish newspaper Yeni Safak, citing the audio, has said his torturers cut off his fingers during an interrogation and later beheaded him.
On Thursday, Prince Mohammed attended the first meeting of a committee aiming to restructure the kingdom's intelligence services after the killing of Khashoggi, the state-run Saudi Press Agency said.
Also on Thursday, Human Rights Watch said that Khashoggi's son, Salah, and his family have left Saudi Arabia for the United States after a travel ban on them was lifted. "Where is it?" Turkish Foreign Minister Mevlut Cavusoglu said at a news conference with his Palestinian counterpart.
According to an Elysee Palace readout of the conversation, Macron pressed his Saudi counterpart for more clarity on what happened to Khashoggi and told him France considers freedom of expression and freedom of the press an "essential priority". They also photographed Saudi diplomatic vehicles scouting wooded areas in the days before Khashoggi disappeared.