Those comments were made in 2017, well before Khashoggi was killed last October in a Saudi consulate in Istanbul, the Times said, citing current and former USA and foreign officials knowledgeable about intelligence reports.
She accused Riyadh of compounding the offence by interfering with Turkey's attempts to investigate.
According to the official who spoke with Channel 13, the Foreign Ministry document, written by the ministry's Center for Political Research, also noted that management of the Palestinian portfolio was shifted from Saudi Crown Prince Mohammed bin Salman to King Salman, who is considered to have more hawkish stances on the Israeli-Palestinian conflict.
Responding to the report, Aldakhil said on Thursday night: "These allegations are categorically false".
During her investigation, Callamard expressed serious concerns over the trial of the 11 accused in the murder case continuing in the Saudi kingdom.
To date, the Saudi authorities have repeatedly failed to disclose the whereabouts of Khashoggi's remains, despite admitting that "he met his death within their custody in their consular premises".
Khashoggi, a Washington Post contributor, was killed on October 2 during a visit to his country's consulate in Istanbul to obtain paperwork ahead of his wedding to Hatice Cengiz.
US intelligence agencies believe the crown prince ordered an operation to kill Khashoggi, a Washington Post columnist and one-time royal insider, whose body was dismembered.
Saudi Arabia has denied the Crown Prince was behind Mr Khashoggi's assassination.
US President Donald Trump has reiterated the Saudi denials and countered the CIA's assessment, refusing to denounce MBS.
A group of Republican and Democratic lawmakers on Thursday renewed their push to penalize Saudi Arabia, unveiled legislation to bar some arms sales and impose sanctions on those responsible for Khashoggi's death. "I believe the United Nations report would have an worldwide impact".
Al-Jubeir reiterated Friday that the prince was not involved in the murder and blaming him would be crossing a "red line".
Suggesting that Congress was holding Saudi Arabia to a higher standard than other countries, Jubeir said, "You've had so many journalists murdered in the previous year, are they going to legislate sanctions against all countries in which journalists have been killed?"
"I wish Congress would take step back", he said.