The official spoke on condition of anonymity because the investigation was ongoing.
On Tuesday, a Turkish Foreign Ministry official acknowledged police want to search the Saudi consul's home as well. Leaked surveillance footage show diplomatic cars traveled to the consul's home shortly after Khashoggi's disappearance at the consulate on October 2.
Trump has threatened "severe punishment" if it turns out Khashoggi was killed in the consulate, but ruled out canceling arms deals worth tens of billions of dollars.
"We're going to try get to the bottom of it very soon but his was a flat denial", Trump told reporters.
"He said that they are working closely with Turkey to find answer".
A report by CNN quoted two sources as saying that the Saudi side is preparing a report to acknowledge that the interrogation of Khashoggi had been meant to abduct him from Turkey, but went wrong and lead to his death.
Many members of the US Congress, which has long had a testy relationship with Saudi Arabia, have issued strong criticism of the kingdom.
Turkish prosecutors have also reiterated that they have the "evidence of killing" at the Saudi consulate.
"Given there seems to be clear evidence that Mr. Khashoggi entered the consulate and has never been seen since, the onus is on the Saudi authorities to reveal what happened to him", Bachelet said.
Pompeo was greeted at the airport by officials including Saudi ambassador to Washington, Prince Khaled bin Salman.
The search came after Turkish President Recep Tayyip Erdogan and King Salman also had their first telephone talks since the controversy erupted, in what appeared to be a conciliatory conversation according to official readouts.
USA top diplomat Mike Pompeo met Tuesday with Saudi King Salman and the crown prince seeking to defuse a crisis over missing journalist Jamal Khashoggi, with American officials saying Riyadh had agreed the need for a "thorough" probe.More news: Trump sends Pompeo to Riyadh over Khashoggi; Saudis may blame official
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CNN said on Monday that after denying for two weeks any role in his disappearance, Saudi Arabia was preparing to say he died in a botched interrogation.
The official said evidence was being shared with countries including Saudi Arabia and the United States.
Investigators, wearing white crime-scene overalls and shoe covers, entered the Istanbul residence of the Saudi consul general, Mohammed al-Otaibi, who has returned to Riyadh.
President Donald Trump said Monday that "rogue killers" may be responsible for his disappearance, adding that Saudi Arabia's King Salman "firmly denied" knowing anything about what happened.
The New York Times reported that the Saudi royal court would suggest that an official within the kingdom's intelligence services, a friend of Prince Mohammed, had carried out the killing.
Khashoggi's disappearance has caused USA -based companies, including Uber, JPMorgan Chase and Google - which planned this year to build five innovation hubs in Saudi Arabia - to pull out of a high-profile investment summit in Riyadh scheduled for later this month. Saudi Arabia has called those allegations "baseless", but has been unable to explain what happened to him.
Turkish investigators had been poised to enter the consulate for days, however the Saudis rescinded their offer of cooperation after the identities of an alleged "hit squad" of 15 Saudis suspected of being involved in Khashoggi's murder were leaked to the press.
Pompeo met King Salman and Crown Prince Mohammed bin Salman in Riyadh to discuss the incident, which has caused global outrage and brought renewed attention on the authoritarian kingdom's human rights record.
"There are other countries we could sell that to", Rubio told CNN.
Saudi Arabia has pledged to retaliate economically for any US punitive action.
The kingdom has not responded to repeated requests for comment from The Associated Press.