Secretary General Antonio Guterres told the BBC he feared such disappearances would happen more regularly and become a “new normal”.
Mr Khashoggi, a critic of the Saudi government, vanished on 2 October after visiting its consulate in Istanbul.
Saudi Arabia says accusations it ordered his killing there are “lies”.
Interior Minister Prince Abdulaziz bin Saud bin Naif bin Abdulaziz, in quotes reported by the official Saudi Press Agency in Friday, said the kingdom was also keen to uncover “the whole truth”, but added that allegations it had issued orders to kill Mr Khashoggi were “baseless”.
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A Turkish security source has told the BBC that officials had audio and video evidence proving Mr Khashoggi, who writes for the Washington Post, was murdered inside the consulate.
US President Donald Trump, who has sought to build good relations with Saudi Arabia, pledged to uncover the truth.
But he ruled out halting big US military contracts with the kingdom on the grounds that jobs would be lost.
Mr Trump on Friday told reporters he would call King Salman of Saudi Arabia to discuss “the terrible situation in Turkey”.
What did Mr Guterres say?
He told me at the International Monetary Fund meeting in Bali: “We need to have a strong request for the truth to be clear.
“We need to know exactly what has happened and we need to know exactly who is responsible and, of course, when we see the multiplication of this kind of situation I think we need to find ways in which accountability is also demanded.”