Deputy Public Prosecutor Shalaan bin Rajih Shalaan did not identify those charged at Thursday’s news conference in Riyadh.
But he said investigations had “revealed that the person who ordered the killing was the head of the negotiations team” sent to ensure Khashoggi returned to Saudi Arabia from his self-imposed exile.
“[The crown prince] did not have any knowledge about it,” he added.
Critics of Prince Mohammed, the son of King Salman and Saudi Arabia’s de facto ruler, believe it is highly unlikely he would not have been aware of the operation.
Several of the 21 people arrested over the murder have been seen in his security detail in the past. Two top advisers have also been sacked over the incident.
Turkey’s President Recep Tayyip Erdogan has also said he believes “the order to kill Khashoggi came from the highest levels of the Saudi government”.
Prince Mohammed has denied any role in the murder, describing it as a “heinous crime that cannot be justified” and vowing that “justice will prevail”.