Speaking to reporters in Washington on Friday, Jubeir argued that the Saudi leadership could not be dictated on how to handle the murder case.
“For anyone to think that they can dictate what we should do, what our leadership should do, is preposterous,” he said. “Our leadership is a red line."
However, Jubeir declined to comment specifically on a newspaper report that the crown prince in 2017 said he would use "a bullet" on the journalist, Presstv Reported.
According to the New York Times on Thursday, the crown prince had told an aide a year before Khashoggi was killed that he would use "a bullet" on the journalist if he did not end his criticism of the government.
Khashoggi was killed last October in a Saudi consulate in Istanbul, with the Times citing current and former US and foreign officials as saying that those comments had been made in 2017.
Asked about the story, Jubeir said: "I can't comment on reports based on anonymous sources. We have seen in the past that many so-called reports based on intelligence sources have not panned out."
Pressed by reporters if he rejected the crown prince having used the phrase in a conversation, Jubeir replied: "It's not about reject or not reject. We know that the crown prince did not order this."
Jubeir said Saudi Arabia's trial of suspects in the case would show that it was a “rogue operation” committed by "officials of the Saudi government acting outside their authority.”
His remarks came as a UN-led inquiry into Khashoggi's murder concluded that evidence pointed to "a brutal and premeditated killing" by Saudi officials.
US intelligence agencies had previously concluded that the heir to the Saudi throne must have at least had knowledge of the assassination plot.
'Trump may miss Khashoggi report deadline'
On Friday, a senior administration official said the US president might not meet the deadline to report to Congress on the case.
“The president maintains his discretion to decline to act on congressional committee requests when appropriate,” the official said in an emailed statement.
“The US Government will continue to consult with Congress and work to hold accountable those responsible for Jamal Khashoggi’s killing.”
Juan Pachon, a spokesman for Senator Bob Menendez, said Trump was actually breaking the law by failing to send the report.
“The administration’s refusal to deal with this issue and keep Congress informed underscores the need to get to the bottom of what is motivating the Trump foreign policy,” said Eliot Engel, chairman of the House of Representatives Foreign Affairs Committee.
Khashoggi — a Washington Post columnist and a late but vocal critic of bin Salman — was killed and his body was dismembered by a Saudi hit squad after being lured into the consulate in Istanbul on October 2, 2018.
After weeks of outright denial, the Riyadh regime eventually acknowledged the murder but has attempted to shift the blame to bin Salman’s underlings and away from the prince himself.
US President Donald Trump insists that Washington-Riyadh ties are more important than establishing accountability for the murder.
However, the Senate gave Trump 120 days — until the end of February 8 — to determine who was responsible for the death of Khashoggi and whether new sanctions should be imposed on Saudi Arabia.