Cengiz contacts Turkish officials to say that Khashoggi has been held or "something bad" has happened to him.
Central Intelligence Agency director Gina Haspel visited the Turkish capital Ankara on Tuesday for talks with officials about the killing of Washington Post contributor Khashoggi inside Saudi Arabia's Istanbul consulate.
When asked about the possible role of Crown Prince Mohammed bin Salman, the president replied: "Well, the prince is running things over there more so at this stage. He's running things and so if anybody were going to be, it would be him".
Saudi Arabia's crown prince struck the tone of outraged leader rather than alleged suspect in his first public speech since the murder of a Saudi journalist in Istanbul three weeks ago.
Addressing a panel at the Future Investment Initiative conference in Riyadh, Prince Mohammed said that many parties were trying to exploit the incident to "drive a wedge between Saudi Arabia and Turkey".
Saudi Arabia's powerful crown prince has called the killing of Jamal Khashoggi a "heinous crime that can not be justified".
The kingdom's announcement that Khashoggi died in a "fistfight" was met with global skepticism and allegations of a cover-up to absolve the 33-year-old crown prince of direct responsibility.
But the president appeared more open on Tuesday to punishing the Saudi government, telling reporters in the Oval Office he would consider jeopardizing military sales if the Saudi government was officially behind the killing.
He was joined by Crown Prince of Bahrain Prince Salman Bin Hamad Al-Khalifa, and Lebanese Prime Minister Saad Hariri.
The Saudi kingdom has provided conflicting accounts of what happened to Khashoggi, a U.S. resident and Washington Post contributor.
On the day of Khashoggi's disappearance, 15 other Saudis, including several officials, arrived in Istanbul on two planes and visited the consulate while he was still inside, according to Turkish police sources.
Turkish pro-government media has claimed that Ankara has audio tapes of the killing.
Crown Prince Muhammad said, "The new Europe is the Middle East. Saudi Arabia and Bahrain will be different, even Qatar despite our differences, they have a strong economy and they will be different in five years".
On Monday, leaked surveillance video showed a man strolling out of the diplomatic post hours after Khashoggi disappeared into the consulate, apparently wearing the columnist's clothes as part of a macabre deception to sow confusion over his fate.
She is expected to speak to King Salman, the head of Saudi Arabia's ruling family, later.