Agency says it is inconceivable Mohammed bin Salman was kept in the dark about Istanbul operation.
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The CIA believes Saudi Crown Prince Mohammed bin Salman ordered the assassination of journalist Jamal Khashoggi, according to US media reports.
The Washington Post said the CIA's assessment was based in part on a phone call the prince's brother, the Saudi ambassador to the United States, had with Khashoggi, telling him to go to the consulate in Istanbul to retrieve documents. He has denied making the call.
Once inside the consulate, Khashoggi was murdered.
In a Twitter post, Khalid bin Salman denied the claims, saying he hadn't spoken to Khashoggi for almost a year before his death.
Saudi Arabia has admitted Khashoggi was killed at the consulate but claims it was accidental. Five suspects have been charged with the murder and are facing the death penalty.
Turkish officials say the death was intentional and are pressuring Riyadh to extradite those responsible.
Earlier this week, the US imposed economic sanctions on 17 Saudi officials for their role in the murder.