The Saudi envoy was called in on Wednesday, they said, to clarify the whereabouts of Khashoggi, a critic of Riyadh's foreign policy and its crackdown on dissent who left Saudi Arabia a year ago saying he feared retribution for his views.
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 crown prince insisted that the kingdom has always paid for armaments from the US.
"Mr. Khashoggi visited the consulate to request paperwork related to his marital status and exited shortly thereafter", the official said.
That the Saudi authorities would potentially risk detaining Khashoggi at a consulate in a country with which ties are already tenuous signals just how important Khashoggi is to Riyadh.
"The information we have is that the Saudi citizen in question is still in the Saudi Arabian consulate in Istanbul", spokesman Ibrahim Kalin said Wednesday.
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Last week, U.S. President Donald Trump said the Saudi King would not last for two weeks in power without U.S. military support. No one at the Saudi embassy in Ankara was available to comment on Thursday and an official at the consulate, asked about the envoy's summons, referred back to the statement.
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"His criticism, voiced over the past year, most surely rankles Mohammed bin Salman, who was elevated to crown prince last year and has carried out a wide-ranging campaign to silence dissent while trying to modernise the kingdom".
But Saudi Arabia claimed he had entered and then left the mission on Tuesday.
He is well-known for his work interviewing Osama bin Laden, for his stint as deputy editor-in-chief of Arab News between 1999 and 2003, and his role as former general manager and editor-in-chief of Al Arab News Channel.
Khashoggi's disappearance threatens to further harm relations between Turkey and Saudi Arabia, which are on opposite sides of an ongoing four-nation boycott of Qatar and other regional crises. In the early 1990s, he tried to persuade bin Laden to reconcile with the Saudi royal family and return home from his base in Sudan, but the al-Qaida leader refused.
Khashoggi's most recent columns for The Washington Post cover some of the most taboo subjects in Saudi Arabia: The need to end the ongoing war in Yemen, the moderate nature of the Muslim Brotherhood, and the need for domestic political reforms beyond allowing women the right to drive.