Turkish and Saudi crime investigators probing the Washington Post contributor’s disappearance left the Saudi consulate after a nine-hour search on Tuesday.
But despite denying being behind Mr Khashoggi’s disappearance, the Saudis are now set to admit he died during interrogation after entering the consulate on October 2, CNN and the New York Times report.
The Saudis will say the operation was carried out “without clearance” from the ruling royal family, CNN reports.
The New York Times claims an unnamed source said the Saudi royal family’s crown prince approved interrogation or rendition of the dissident Mr Khashoggi back to Saudi Arabia.
It says the Saudi government will blame an intelligence official for the bungled operation.
Mr Khashoggi had been a vocal critic of the Saudi Arabia ruling royal family.
Donald Trump had previously suggested “rogue killers” could be behind Mr Khashoggi’s disappearance.
Speaking at a trip to survey hurricane damage in Florida on Monday, Mr Trump admitted he had heard the reports of an imminent Saudi admission, but said “it’s just a rumour of a report coming out”.
The president has sent US Secretary of State Mike Pompeo to meet Saudi King Salman in a case that has strained White House ties with the Saudis.
On Monday, Mr Trump tweeted: “Just spoke to the King of Saudi Arabia who denies any knowledge of whatever may have happened “to our Saudi Arabian citizen.
“He said that they are working closely with Turkey to find answer.
“I am immediately sending our Secretary of State to meet with King!”
The Turkish crime investigation team of around 10 people left the consulate around 5am on Tuesday.
Mr Khashoggi, a US resident, vanished after entering the consulate to get marriage documents.
Turkish officials believe he was murdered there and his body removed with the case provoking an international outcry against Saudi Arabia.
In a statement released on Monday, Mr Khashoggi’s family said: “We are sadly and anxiously following the conflicting news regarding the fate of our father after losing contact with him two weeks ago.
“The strong moral and legal responsibility which our father instilled in us obliges us to call for the establishment of an independent and impartial international commission to inquire into the circumstances of his death.”