That earlier assertion, in turn, backtracked from an initial statement that Saudi authorities knew nothing about what happened to the columnist for The Washington Post, who vanished after entering the consulate October 2.
He said a team of Saudi agents arrived in Turkey on October 1, the day before Khashoggi's death, and some visited the woods around Istanbul; that area has been searched for the journalist's body, which has yet to be found.
In Saudi Arabia, the crown prince addressed the crisis publicly for the first time at an investors conference Wednesday, calling the killing a "heinous" crime that was a "very, very painful incident for all Saudis".
Saudi Arabia has said that 18 people had been arrested in connection with the incident.
Iranian President Hassan Rouhani said on Wednesday that the killing of the Saudi journalist Jamal Khashoggi was supported by the United States, official IRNA news agency reported.
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"The ideal thing for Trump to do is recognize that Mohammed bin Salman is weakened by the outrageous murder of Khashoggi", said Indyk, who argues that the one threat to the crown prince's survival is if the United States tells Saudi Arabia's King it can not work with his heir apparent.
"I want to send them a message that they can not do this as long as there is a king named Salman bin Abdul Aziz and a crown prince named Mohammed bin Salman in Saudi Arabia, and a president in Turkey named Erdogan".
"We will prove to the world that the two governments (Saudi and Turkish) are cooperating to punish any criminal, any culprit, and at the end justice will prevail", he said to applause.
Khashoggi's eldest son, Salah, has flown out of Saudi Arabia, two sources close to the family said on Thursday.
For their part, the Trump administration and the USA defence industry are scrambling to save the few actual deals in a much-touted $110 billion arms package for Saudi Arabia.
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Saudi officials said the crown prince also called Turkish President Recep Tayyip Erdogan on Wednesday to discuss the investigation.
France has said it will consider sanctions against Saudi Arabia if its intelligence services find Riyadh was behind Khashoggi's death.
"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". He joked about Hariri's detention in the kingdom previous year, saying the Lebanese prime minister was free to leave after attending the conference.
Saudi officials have also said the crown prince had no knowledge of the killing.
He seemed relaxed on the panel he shared with Bahrain's Crown Prince Salman bin Hamad al-Khalifa and Lebanon's Prime Minister Saad al-Hariri.
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But Turkey wants more answers from Saudi Arabia, a regional rival that is also a source of investment.