Speaking to reporters in Nevada, Trump added that it was possible that Saudi Crown Prince Mohamed bin Salman had been unaware of the death.
Trump chose Saudi Arabia as his first overseas destination as president, and his son-in-law and adviser Jared Kushner has developed close ties with Prince Mohammed, apparently seeing him as an ally in advancing his yet-to-be-released peace plan for Israel and the Palestinians.
The comments from Foreign Minister Adel al-Jubeir were some of the most direct yet from Riyadh which has given multiple and conflicting accounts about Khashoggi's killing on Oct.2, first denying his death before admitting it on Saturday amid an worldwide outcry.
After denying any knowledge of Khashoggi's whereabouts for two weeks, Saudi Arabia admitted on Friday that the journalist died in a fight inside its consulate.
Condoling with Khashoggi's family, Saudi Arabia's top diplomat said, "This is a awful mistake".
The Saudi official on Sunday told ABC News that Khashoggi's body was given to a "local cooperator" in Istanbul for disposal.
However, he made it clear that he believed the murder was directed by the prince, who has consolidated power in the world's top oil exporter and courted US President Donald Trump.
He said it was premature to discuss sanctions, in line with Trump administration efforts to censure a killing that has drawn worldwide outrage while also protecting relations with the Saudis. "You'll never convince me that he didn't do this". "Our condolences go out to them, we feel their pain", Mr Jubeir said. "This was an operation that was a rogue operation", he said.
Turkish President Tayyip Erdogan speaks during a ceremony in Istanbul Turkey
Kentucky GOP Sen. Rand Paul, a member of the Senate Foreign Relations Committee, said in an interview on "Fox News Sunday" that a full discussion of the US-Saudi relationship should be underway and called for an end to arms sales, invoking the use of US-arms by the Saudi-led coalition in Yemen and the humanitarian crisis there. "The Saudis have said a lot of crap that's not right, accurate or true - we know that".
"Now they're engaged in a cover up to protect the Crown Prince, and we'll see how that works for them", the Virginia Democrat told CNN's Kate Bolduan on "Erin Burnett OutFront".
Canada condemned Saudi Arabia's account of the death of dissident journalist Jamal Khashoggi as inconsistent and not credible on Saturday, calling for a "thorough" investigation.
Fifteen Saudis, members of the team sent to Turkey to meet with Khashoggi in the consulate in Istanbul, are among those who have been detained by the Saudi public prosecutor, according to the official.
Sceptics have asked why so many people, including military officers and a forensics expert specialising in autopsies, were part of the operation if the objective was to convince Khashoggi to return home of his own volition.
The evolving explanation comes 19 days after Khashoggi, a Saudi journalist who had been critical of his country's current government, disappeared on October 2 after going into the Saudi consulate in Istanbul.