The killing has strained relations between the USA and Saudi Arabia.
"Consistent with the previous administration's position and the constitutional separation of powers, the president maintains his discretion to decline to act on congressional committee requests when appropriate", a senior administration official said.
He was a strong critic of the Saudi government.
In this Thursday, April 27, 2017 photo released by Saudi Press agency, SPA, Saudi Defense Minister and Deputy Crown Prince Mohammed bin Salman reacts during the opening of the Gulf Cooperation Countries, GCC, Interior, Foreign, Defence Ministers Joint Meeting in Riyadh, Saudi Arabia.
The Saudi government has denied the crown prince played any role in the killing.
His body was reportedly dismembered and has still not been found.
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Watson's representatives declined to provide further documentation and said their client would not be talking to journalists. According to Watson's statement, the two were friends at Duke but never dated or had a romantic relationship.
The comments were intercepted by American intelligence agencies, the newspaper reported.
Meanwhile, the United Nation's special rapporteur on extrajudicial killings, Agnes Callamard, leading the investigations into Khashoggi's death, on Thursday confirmed that evidence showed the latter to be a victim of "a brutal and premeditated killing, planned and perpetrated by officials of the state of Saudi Arabia".
A department spokesman pointed to last year's revocation of visas for almost two dozen Saudi officials and the freezing of assets of 17 others after Khashoggi's murder.
The brutal killing - described by Turkish and USA officials as an elaborate plot - has drawn an worldwide outcry about press freedom and Saudi government tactics to quell criticism.
Congressional leaders triggered the Magnitsky Act in October, giving the administration 120 days, until February 8, to report back on who was responsible for the death of Khashoggi, a US resident killed at the Saudi consulate in Istanbul, Turkey, and whether it would impose sanctions on that person or persons.
Speaking at the launch of a book about the journalist, Hatice Cengiz also said she believes that Saudi King Salman "has a conscience" and will support Turkey's efforts to shed light on his killing. It's unclear if they remain detained during the trial or where they're being held.
But the effort has been mired in the fallout of the Kingdom's October 2 killing of Washington Post columnist Jamal Khashoggi, who was brutally murdered shortly after he entered the Saudi Consulate in Istanbul.
The State Department said Thursday Washington had already taken action, pointing to last year's revocation of visas for almost two dozen Saudi officials and the freezing of assets of 17 others.