A second jet, with registration HZ-SK2, carried another batch of the 15 suspects, but was searched as by then the alarm had been raised that they might be behind Khashoggi's disappearance.
Authorities in Turkey have yet to confirm or deny the existence of a rumored audio recording of the killing from inside the consulate.
They added that it was "hard to imagine what crime the Saudi government would need to commit" for it to be condemned by ministers.
Saudi authorities announced that Jamal Khashoggi, a Washington Post columnist, died in the Saudi Consulate in Istanbul after a fistfight with officials there.
Khashoggi speaks during an interview at an undisclosed location.
As Saudi Arabia faced intensifying global scepticism over its story about the death of journalist Jamal Khashoggi, a senior government official laid out a new version of the death inside the Saudi consulate in Istanbul that contradicts previous explanations.
Hatice Cengiz, a Turkish national, waited for Khashoggi outside the Saudi consulate in Istanbul on October 2, where he was to get papers for their planned marriage.
The latest account includes details on how 15 Saudis sent to confront Khashoggi had threatened him with being drugged and kidnapped and killed him in a chokehold when he resisted.
However, the new narrative - that Khashoggi was accidentally strangled after a brawl erupted between him and officials inside the consulate - was greeted with scepticism and condemnation from the worldwide community.
Saudi Arabia so far has not acknowledged or explained Mutreb's presence in Istanbul nor that of a forensics and autopsy expert, also on hand for Khashoggi's arrival at the consulate on 2 October.
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The king offered his condolences in a telephone call made by him to Mr Jamal Khashoggi's son, Mr Salah Jamal Khashoggi.
The man in the video was identified by a Turkish official, according to CNN, as Mustafa al Madani.
Merkel told reporters in Berlin on Sunday that "I agree with all those who say that the already limited arms exports. can't take place in the situation we're now in".
Asked about Saudi Arabia's belated acknowledgment of Khashoggi's killing, Jubeir said the shifting Saudi account of what happened was a result of a coverup by the arrested agents.
That explanation will face a fresh challenge on Tuesday when Turkish President Recep Tayyip Erdogan is expected to reveal details of his government's investigation into the killing of Khashoggi, a move that could directly contradict Saudi Arabia's official account of what happened inside its consulate.
"We have relatively limited spare capacities and we are using a significant part of them", he said.
"First, we condemn this act in the strongest terms", she said at a news conference on Sunday.
Five Turkish employees of the consulate also gave testimonies to prosecutors on Monday, Turkish media reported.
The calls came as the journalist's fiancée, Hatice Cengiz, was placed under 24-hour police protection, the Istanbul Governor's office announced on Sunday.
On Sunday, Britain, Germany and France issued a joint statement indicating that the Saudi explanation of Khashoggi's killing did not go far enough.