The report released by the Biden administration says the prince approved a plan to either "capture or kill" Khashoggi.
The US announced sanctions on dozens of Saudis but not the prince himself.
Saudi Arabia rejected the report, calling it "negative, false and unacceptable".
Crown Prince Mohammed, who is effectively the kingdom's ruler, has denied any role in the murder.
Khashoggi was killed while visiting the Saudi consulate in Istanbul, Turkey, and his body cut up.
The 59-year-old journalist had once been an adviser to the Saudi government and close to the royal family but he fell out of favour and went into self-imposed exile in the US in 2017.