The comments come after Sky sources said body parts belonging to the Washington Post columnist had been found and Turkish president Recep Tayyip Erdogan called Mr Khashoggi’s killing a premeditated “murder”.
Speaking on Tuesday at the Oval Office, the US leader said his Turkish counterpart had been “pretty rough” on Saudi Arabia when he addressed the writer’s killing in parliament earlier in the day.
President Erdogan demanded Saudi Arabia hold those responsible to account and asked: “Why has the body of someone who was officially said to be killed not been found yet?”
Turkish authorities claim to have an audio recording of Mr Khashoggi’s death that supposedly confirms he was tortured, killed, had his fingers cut off and was dismembered. However, Mr Erdogan did not mention it during his address.
When asked if he believed Mr Erdogan, President Trump said he wanted to see the facts first. But he also said consequences for Saudi Arabia would be decided by congress in consultation with himself.
The US leader criticised the kingdom for one of the “worst cover-ups in the history of cover-ups”.
He said: “Bad deal, should have never been thought of. Somebody really messed up.”
He added: “Whoever thought of that idea I think is in big trouble – and they should be in big trouble.”
The US State Department has since said 21 Saudi officials will have their visas revoked or be made ineligible for US visas over Mr Khashoggi’s death.
Secretary of state Mike Pompeo said the Saudis had been identified in connection with the journalist’s death.
He told reporters: “These penalties will not be the last word on the matter from the United States.
“We’re making very clear that the United States does not tolerate this kind of ruthless action to silence Mr Khashoggi, a journalist, through violence.”
The US leader, who sent his CIA director Gina Haspel to Istanbul to discuss the issue, is expecting a full report in the coming days.
Riyadh originally said Mr Khashoggi had left the Saudi consulate unharmed on 2 October. He had last been seen entering the building.
About two weeks after his disappearance, Saudi Arabia then claimed the journalist – a staunch critic of the kingdom – died accidentally in a “fist fight” inside the consulate.
However, Turkish authorities maintain a 15-man team tortured and killed Mr Khashoggi.