When the Turkish investigators entered the consulate, some wearing white protective gear, they "smelled chemicals had been used", according to two officials in contact with the investigators. The New York Times reported that Prince Mohammed had approved an interrogation or abduction of Khashoggi and the government would shield him by blaming an intelligence official.
Khashoggi, 59, had been living in the US for a year in self-imposed exile and writing columns for the opinion section of The Washington Post.
Mr Trump says "rogue killers" could be responsible for his disappearance because the Saudi ruler King Salman has denied knowing what happened.
The Saudis have strongly denied the accusations, but USA media outlets have reported that they will acknowledge Khashoggi was killed in a botched interrogation.
Under increasing global pressure, Saudi Arabia is reportedly trying to piece together an alibi over Khashoggi's disappearance. Turkish officials say they believe he was murdered there and his body removed. Those are all indications Trump is sticking by Saudi Arabia, the first country he visited as president in 2017. He was last seen entering the Saudi consulate in Istanbul where he went to receive papers he needed to remarry.
Iran, as the regional rival to Saudi Arabia, would be the prime beneficiary if the Saudis were to lose their defensive U.S. umbrella.
The Associated Press, citing Turkish police sources, reported the evidence indicated Khashoggi was killed at the consulate, where he visited October 2 get a document needed so he could marry.
Trump over the past several days has repeatedly touted denials from the king and crown prince over Khashoggi's disappearance. Maybe I don't want to get into his mind, but it sounded to me like maybe these could have been rogue killers - who knows?
Trump quoted the King on Monday as saying that neither he nor his son, the crown prince, had any information about what had happened to Khashoggi.
A Turkish prosecutor left around one and a half hours later, followed shortly after by a Saudi team that departed in three vehicles, another witness said. The Trump administration's ongoing courtship of Saudi Arabia is on pause.
Trump has threatened "severe punishment" if it turns out Khashoggi was killed in the consulate, although he has ruled out cancelling arms deals worth tens of billions of dollars with Saudi Arabia.
Saudi Arabia has denied killing him and initially said he left the building unharmed.
Bahraini Prime Minister Prince Khalifa bin Salman Al-Khalifa affirmed the nation's strong support of the firm Saudi stance against any attempt or threats to undermine it, expressing strong condemnation of the false claims against the Kingdom by some media outlets. "Here we go again with, you know, you're guilty until proven innocent. They were very clear: they understand the important of this issue, they are determined to get to the bottom of it", Pompeo told reporters.
In August, Saudi Arabia reacted strongly to a tweet from Freeland calling for the immediate release of detained activists, including Samar Badawi, a champion of women's rights and the sister of detained blogger Raif Badawi.
Meanwhile, International Monetary Fund chief Christine Lagarde has become the latest high-profile figure to withdraw from a major Saudi investment conference next week following Mr Khashoggi's disappearance.
After critical talks in Riyadh Tuesday, Pomepeo was expected in Turkey on Wednesday to meet Turkish Foreign Minister Mevlut Cavusoglu, the state-run Anadolu news agency said.