Investigations into his disappearance earlier in the month are continuing, and 18 Saudi nationals have been detained, according to the Saudi Foreign Ministry.
The kingdom also fired several intelligence officers including some close to Crown Prince Mohammed bin Salman, the ministry said, though it made no reference to the crown prince's possible involvement in the case.
"The kingdom expresses its deep regret at the painful outcome and stresses the commitment of the authorities in the kingdom to bring the facts to the public," it said in a statement.
U.S. President Donald Trump said Friday he thinks the Saudi's account is "credible" but that what happened to Khashoggi is "unacceptable."
Trump told reporters in Arizona that he could consider imposing sanctions on Saudi Arabia. But he appeared unwilling to get too tough on the nation's key ally in the Middle East, given Riyadh's role in countering Iran's influence in the region and as a major buyer of U.S. military equipment.
Khashoggi, a columnist for the Washington Post who had been critical of Saudi Arabia's royal family, vanished after entering the Saudi consulate in Istanbul on Oct. 2.
U.S. media have reported that Turkish investigators heard audio recordings that suggested Khashoggi was tortured and killed.
White House press secretary Sarah Huckabee Sanders said Friday the United States "will continue to closely follow the international investigations into this tragic incident and advocate for justice that is timely, transparent, and in accordance with all due process."