The statement came after Trump said he would be receiving a full report on the killing in the Saudi Consulate in Istanbul last month, and after the Washington Post reported that the CIA had assessed with high confidence that the Crown Prince ordered Khashoggi's death.
No intelligence from the CIA was presented in the report, and Trump said the agency was still looking into the issue.
In the eight-paragraph statement, the President lauded Saudi Arabia's economic ties with the United States and emphasised the country's opposition to Iran.
He noted that Saudi Arabia considered Khashoggi an "enemy of the state" and a member of the Muslim Brotherhood but insisted that "my decision was in no way based on that".
He dismissed suggestions that he slash arms deals with Saudi Arabia, saying Russia and China would benefit instead.
The President seemed to pre-empt likely criticism from Congress, where a number of pending bills seek to punish Saudi Arabia. Some of Trump's allies, including Senator Lindsey Graham, have said Mohammed has no credibility and they will not deal with him in the future.
"I understand there are members of Congress who, for political or other reasons, would like to go in a different direction — and they are free to do so. I will consider whatever ideas are presented to me, but only if they are consistent with the absolute security and safety of America," Trump said.
Despite the CIA conclusion, he said, "we may never know all the facts surrounding the murder of Mr Jamal Khashoggi. In any case, our relationship is with the kingdom of Saudi Arabia. They have been a great ally in our very important fight against Iran."
The United States, he said, "intends to remain a steadfast partner of Saudi Arabia".
