Sources close to the CIA said it had assessed the evidence in detail.
It is understood there is no “smoking gun” but US officials think such an operation would need the crown prince’s approval.
However, Saudi Arabia has called the claim false and insisted that Prince Mohammed knew nothing about plans for the killing.
Saudi Arabia insists Jamal Khashoggi was killed as a result of a “rogue operation”.
The White House says President Donald Trump has spoken to CIA Director Gina Haspel and Secretary of State Mike Pompeo about the CIA’s assessment of the Khashoggi murder.
Press secretary Sarah Sanders gave no details but said President Trump had confidence in the CIA.
Before the briefing, the president stressed the importance of Saudi Arabia to the United States, as he has done since news of Jamal Khashoggi’s killing emerged.
While there has been widespread international condemnation of Jamal Khashoggi’s murder there has been little in the way of substantial action.
Jamal Khashoggi was killed after entering the Saudi consulate in Istanbul on October 2 to obtain a marriage document. The journalist’s body has not been found.
Turkey also insists the order to the Saudi dissident came from the highest levels.
The Washington Post, which Jamal Khashoggi worked for, says the CIA assessment was based partly on a phone call made by the crown prince’s brother, Prince Khalid bin Salman, the Saudi ambassador to the US.
Prince Khalid allegedly called Jamal Khashoggi at the direction of his brother and gave him assurances that he would be safe to go to the consulate.
However, Prince Khalid, now back in Saudi Arabia, tweeted that he had not been in contact with Jamal Khashoggi for nearly a year.
The prince said he had never suggested Jamal Khashoggi – who had been in London for a conference until the day before his disappearance – should go to Turkey for any reason.
It is understood CIA agents have also examined a call made to a senior aide of Crown Prince Mohammed by the team that carried out the killing.
Sources quoted in the media stressed that there was no single piece of evidence linking Crown Prince Mohammed directly to the murder, but officials believe such an operation would have needed his approval.
At a news conference in Riyadh on November 15, Deputy Public Prosecutor Shalaan bin Rajih Shalaan said Jamal Khashoggi was given a lethal injection and his body was dismembered inside the consulate after his death.
The body parts were then handed over to a local “collaborator” outside the grounds, the prosecutor added.
A composite sketch of the collaborator has been produced and investigations are continuing to locate the remains.
Eleven unidentified people have been charged over Jamal Khashoggi’s death and the prosecutor is seeking the death penalty for five of them.
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