Sherif Mansour, Middle East and North Africa program coordinator for the Committee to Protect Journalists, said Khashoggi's failure to emerge from the consulate "is a cause for alarm", given the Saudi authorities' pattern of "quietly detaining critical journalists".
A Turkish official told the AP late Saturday that an "initial assessment" by police concluded Khashoggi had been killed at the consulate.
The Saudi consul-general in Istanbul allowed reporters from the Reuters news agency to tour the consulate on Friday, to show that Khashoggi was not on the premises.
Lebanon's Al Akhbar newspaper cited an Arab source as saying Saudi Arabia had informed Turkey that Khashoggi was now in the Saudi capital Riyadh. The Lebanese al-Akhbar newspaper said that the journalist had been flown to Saudi Arabia with the apparent consent of the Turkish intelligence authorities.
Ankara says there was no proof he left the mission.
Fearing he would be arrested or banned from traveling outside the kingdom, Mr. Khashoggi left his home country previous year and moved to Washington, D.C., where he lived in self-imposed exile.
Khashoggi has been a vociferous critic of Prince Mohammed's policies in both the Arab and Western press.
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Rights groups have called on Saudi Arabia to verify Khashoggi's whereabouts, with Human Rights Watch calling on Turkey to deepen its investigation into the case, saying if Saudi Arabia had detained Khashoggi without acknowledging it, his detention would constitute an enforced disappearance.
The killing, if confirmed, would mark a stunning escalation of Saudi Arabia's effort to silence dissent.
Turkish officials said the Saudi side didn't provide video footage or other evidence to support that claim.
President Recep Tayyip Erdogan is expected to release a statement on Sunday, according to The Guardian. But Turan Kislakci added that diplomatic cars had been seen moving in and out. 'We have nothing to hide'.
Yasin Aktay told broadcaster CNN Turk that Khashoggi had not left the Saudi consulate in Istanbul, which he had entered on Tuesday to obtain documents for a forthcoming marriage, in "normal ways".
In an article published by Al-Jazeera this week, journalist and analyst Bill Law described Khashoggi as "a brilliant journalist with a fiercely independent mind but with sufficient pragmatism to know just how close to the red lines he could go".
Khashoggi fled from Saudi Arabia in September 2017, months after Prince Mohammed was appointed heir to the throne, amid a campaign that saw dozens of dissidents arrested including intellectuals and Islamic preachers.
"Mr. Jamal is a journalist friend I have known for a very long time, therefore I still hope for a positive outcome", Erdoğan said speaking to the press.