Kushner and national security adviser John Bolton had called bin Salman almost a week after Khashoggi went missing from the Saudi consulate in Istanbul, Turkey, and amid an investigation into the journalist's disappearance, CNN reported in October.
Kushner, who is Trump's son-in-law, was singled out by Saudi officials seeking to take advantage of the incoming administration's lack of political experience and ambitions for the Middle East, according to The New York Times, which cited senior officials Saturday as well as documents, emails and text messages.
The White House reimposed rules that insisted National Security Council staffers be included on calls with foreign leaders, they said.
Despite speculation that the powerful crown prince ordered the hit, the kingdom has strongly denied he was involved.
His disappearance sparked harsh backlash against the Saudi government as evidence mounted that the Saudis were behind the killing.
A Saudi delegation met with Kushner as early as November 2016, the month Trump was elected president, according to the report.
There is also an indication that phone calls were made - possibly to Riyadh - to report on the process of the murder scene.
Kushner's support for Prince Mohammed in the moment of crisis is a striking demonstration of a singular bond that has helped draw President Trump into an embrace of Saudi Arabia as one of his most important global allies. The CIA has concluded that the prince, often known by the initials MBS, played a role in the killing.
It appears to have been the first face-to-face meeting between Kushner and the prince, but Kushner raised eyebrows by telling others in the White House that he and Prince Mohammed had already spoken several times before, two people at the event recalled.
While Kushner continues to push that the USA must stand by bin Salman, it is unsure whether he can be the key to the Trump administration's Middle East strategy.
White House officials declined to comment on Kushner's one-on-one communications with the prince since the killing of Khashoggi.
But Haley's remarks lose all their luster when considering she outright refused to single out Saudi Crown Prince Mohammed bin Salman, despite numerous reports from US Intelligence agencies directly linking the Saudi prince to the gruesome killing.