Khashoggi was murdered on October 2 in the Saudi consulate in Istanbul. Officials told US media such an operation would have needed the prince's approval.
"They didn't conclude," Trump said on Thursday when asked about the CIA's evaluation by reporters at Mar-a-Lago in Florida, BBC reported.
"They have feelings certain ways. I have the report, they have not concluded, I don't know if anyone's going to be able to conclude the crown prince did it," he said.
The President has repeatedly stressed the importance of Saudi Arabia to the US following the killing.
Earlier this week, Trump released a statement suggesting that the crown prince "could very well" have known about the incident.
His statement said: "(It) could very well be that the crown prince had knowledge of this tragic event - maybe he did and maybe he didn't!"
On November 17, White House Press Secretary Sarah Sanders told reporters that Trump had confidence in the CIA following conversations with Director Gina Haspel and Secretary of State Mike Pompeo about the Khashoggi murder.
Sources quoted in the US media at the time stressed that there was no single piece of evidence linking the crown prince directly to the murder, but officials believed the killing would have required his endorsement.
Saudi Arabia called the claim false and insisted that the crown prince knew nothing about plans for the killing.
The Gulf kingdom's public prosecutor says Khashoggi was killed as a result of a "rogue operation".
However, the Hurriyet newspaper reported on Thursday that Ms Haspel told Turkish officials last month the CIA had a recording in which the crown prince gave instructions to "silence" the Saudi writer as soon as possible.
When asked about the claims by reporters, Trump said: "I don't want to talk about it. You'll have to ask them."
The Saudi crown prince left on a visit to "brotherly Arab states" on Thursday, Saudi state media reported, beginning a regional tour with the United Arab Emirates.
It will be his first official trip abroad since Khashoggi was killed.
The crown prince is also expected to participate in a G20 meeting of world leaders in Buenos Aires, Argentina, at the end of the month that will be attended by leaders from the US, Turkey and a number of European countries.
Meanwhile, France has announced that it is imposing sanctions on 18 Saudi nationals -- the same individuals targeted with sanctions by the US, UK and Germany - allegedly linked to the Khashoggi murder.
Their list of individuals does not include the crown prince, a spokesperson for the French ministry of foreign affairs said.
