An investigation revealed that, on Tuesday morning, the day when Khashoggi was scheduled to return to the consulate, 12 Saudi officials arrived in Istanbul in two private jets, and went to the consulate.
"We call for cooperation between Turkey and Saudi Arabia to conduct a prompt and impartial investigation into the circumstances of Mr Khashoggi's disappearance and to make the findings public", United Nations human rights spokeswoman Ravina Shamdasani told a Geneva news briefing.
A statement on Sunday by the state-run Saudi Press Agency (SPA) cited a diplomatic officer who categorically denied "these baseless allegations, and expressed his doubt that they came from Turkish officials that are informed of the investigation or are authorised to comment on the issue". "The consulate officials can not save themselves by simply saying "he has left", Erdogan told a news conference in Budapest, where he is on an official visit.
That harshness corresponds with the growing concerns internationally about the direction Saudi Arabia is taking under Prince Mohammed and his father.
Erdogan said police are looking at surveillance video of the consulate's entrances and exits, as well as at the Istanbul airport.
Two senior administration officials said the administration has no verifiable information to confirm the Turkish government claims that Khashoggi was killed but that the USA is seeking answers about his whereabouts - and talking to senior levels of Saudi government.
His firsthand knowledge of the region and nexus with all kinds of people wielding authority made him suitable to be handpicked in an advisory capacity for the Saudi intelligence and he regularly advised the Saudi intelligence chief, Prince Turki al Faisal on sensitive matters.
He added that he has not yet spoken with Saudi Arabian officials about the case, which happened a week ago.
Even President Donald Trump, who took his first overseas trip as United States president to the kingdom and whose son-in-law Jared Kushner has close ties to Prince Mohammed, said he had concerns.
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The journalist said he had been banned from writing in the pan-Arab daily Al-Hayat, owned by Saudi prince Khaled bin Sultan al-Saud, over his defence of the Muslim Brotherhood which Riyadh has blacklisted as a terrorist organisation.
Why it matters: The incident threatens a diplomatic crisis in Turkey's relations with Saudi Arabia.
But if Khashoggi is dead, the Saudi government certainly had a motive to kill him.
"Right now nobody knows anything about it, but there's some pretty bad stories going around".
The case has sparked an global human rights outcry and calls for both sides to prove their statements.
It was the second time in two days that the ambassador had been questioned by the Foreign Office about what the Saudi royal family may know about Khashoggi's disappearance.
Turkish President Recep Tayyip Erdogan has challenged Saudi Arabia to provide proof that a missing journalist has left its consulate in Istanbul.