A Saudi Embassy spokeswoman said in a statement that "the claims in this purported assessment are false. We have and continue to hear various theories without seeing the primary basis for these speculations."
The Washington Post was first to report on the CIA's assessment.
According to the Post, US officials have high confidence in the CIA's assessment.
A spokesman for the CIA declined to comment to the Post. The Saudi government has denied bin Salman's involvement in Khashoggi's death.
Vice President Mike Pence said the United States would hold all involved with Khashoggi's murder to account. He also said he wanted to preserve the strong relationship with Saudi Arabia amid the murder investigation.
"The murder of Jamal Khashoggi was an atrocity. It was also an affront to a free and independent press and the United States is determined to hold all of those accountable who are responsible for that murder," Pence said.
Khashoggi, a former Saudi royal insider who became a critic of the country's government, went missing in October after he visited the Saudi consulate in Istanbul to obtain papers for his upcoming marriage. The Saudi government offered changing explanations for Khashoggi's disappearance.
Included in the US intelligence analyzed by the CIA was a phone call the prince's brother Khalid bin Salman made to Khashoggi, encouraging the journalist to make the trip to the consulate to get the documents, according to the Post. Sources told the Post that Khalid made the call at his brother's command.
Khalid denied the Post's reporting, saying on Twitter that he had never spoken to Khashoggi by phone.
"I never talked to him by phone and certainly never suggested he go to Turkey for any reason. I ask the US government to release any information regarding this claim," Khalid said.
He said the last contact he'd had with Khashoggi was via text in October 2017.
Fatimah Baeshen, a spokeswoman for the Saudi Embassy in Washington, told the Post that Khalid, who is the Saudi ambassador to the US, and Khashoggi never discussed "anything related to going to Turkey."
US issues sanctions on 17
The CIA also examined an audio recording from inside the Saudi consulate provided by Turkey and a phone call placed from inside the consulate after Khashoggi was killed, according to the Post.
Maher Mutreb, an alleged member of the Saudi hit team and a security official for the crown prince, placed the phone call to a top aide for bin Salman informing the aide that the job had been done, people familiar with the call told the newspaper.
The CIA does not know the location of Khashoggi's remains, according to the Post.
The Trump administration on Thursday imposed penalties on 17 individuals over their alleged roles in the killing of Khashoggi. Khashoggi's assassination has created a crisis for the Trump administration and drawn attention to President Donald Trump's business ties to Saudi Arabia and the relationship between bin Salman and Trump's son-in-law and senior adviser, Jared Kushner.
Earlier Thursday, the Saudi Public Prosecutor's Office said 11 people had been charged for their involvement in the death of Khashoggi, adding that five are facing capital punishment for being directly involved in "ordering and executing the crime."
Khashoggi was killed following "a fight and a quarrel" at the Saudi consulate, the prosecutor's office claimed. Prosecutors said Khashoggi was tied up and injected with an overdose of a sedative that killed him. Then, according to prosecutors, his body was dismembered and removed from the consulate by five people.