WASHINGTON—The Central Intelligence Agency has concluded that the killing of Saudi journalist Jamal Khashoggi was carried out under the orders of Saudi Crown Prince Mohammed bin Salman, a close ally of President Trump, U.S. officials familiar with the matter said.

The determination by the top U.S. spy agency could endanger President Trump’s efforts to protect relations with the crown prince and Saudi Arabia more generally. Mr. Trump said Saturday he expected to receive a briefing from the CIA later in the day.

The...