Officials said they believe 59-year-old Khashoggi's death was planned and Saudi officials had travelled to Istanbul from Riyadh after receiving word that he was going to visit the consulate to sign divorce papers.
He reached the consulate on Tuesday to secure documentation for a forthcoming marriage, according to his fiancée, who waited outside. The official strongly denounced these baseless allegations and expressed his doubt that they came from Turkish officials that are informed of the investigation or are authorized to comment on the issue.
Within a day, Turkish officials were saying they had no evidence that Khashoggi had ever left the consulate while Saudi officials were insisting that the journalist had left fairly quickly. "We believe that the murder was premeditated and the body was subsequently moved out of the consulate", one of two Turkish officials told Reuters on Saturday.
The Saudi source said that a security team including Saudi investigators had arrived in Istanbul on Saturday to take part in the investigation into Khashoggi's disappearance.
Saudi Arabia's consul-general rejected claims about a possible abduction, telling Reuters that his country was helping search for Khashoggi.
Police, also quoted by Anadolu, said that Khashoggi "did not come back out" of the consulate after entering the building.
Jamal Khashoggi is a high-profile critic of Saudi Arabia's Crown Prince Mohammed bin Salman.
A former government adviser who has been critical of some policies of Saudi Crown Prince Mohammed bin Salman and Riyadh's intervention in the war in Yemen, Mr Khashoggi has lived in self-imposed exile in the United States since previous year to avoid possible arrest.
The Committee to Protect Journalists said it was alarmed by reports Khashoggi may have been killed inside the consulate.
"The idea of kidnapping of a Saudi citizen by a diplomatic mission is something that should not be [propagated] in the media" he said.
The disappearance of Khashoggi could threaten the already fragile relationship between Saudi Arabia and Turkey.
The official did not provide details on how the body had been carried out or whether it had been found. Turkey has supported Qatar amid a yearlong boycott by Bahrain, Egypt, Saudi Arabia and the United Arab Emirates over a political dispute. But Saudi Arabia has arguably become Donald Trump's closest ally in the Middle East - and Washington may be reluctant to weigh in against Riyadh at this stage.
The Washington Post chose to leave a blank space where Khashoggi's column would have been in its Friday edition in support of the missing writer.
Human rights groups have urged Riyadh to shed light on Khashoggi's whereabouts.
After several of his friends were arrested, his column was cancelled by the al-Hayat newspaper and he was allegedly warned to stop tweeting, Mr Khashoggi left Saudi Arabia for the United States, from where he wrote opinion pieces for the Washington Post and continued to appear on Arab and Western TV channels.