"We were deeply saddened by the news of Mr Khashoggi's murder and condemn this act against humanity and also journalism and free speech. This was a horrific and deeply regrettable act," said Masayoshi Son in his first comments on the killing.
However, he added: "As horrible as this event was, we cannot turn our backs on the Saudi people as we work to help them in their continued efforts to reform and modernise their society."
Son confirmed he boycotted a high-profile Saudi investment forum last month along with dozens of global business titans after reports emerged that Khashoggi was killed in the Saudi consulate in Turkey.
And he said he had sought explanations from senior Saudi officials over the killing, stressing: "We want to see those responsible held accountable."
Nevertheless, he said the firm took seriously its "obligation" to help the Saudi people "manage their financial resources and diversify their economy".
Son finally broke his silence over the killing after the firm's share price tumbled due to SoftBank's close ties with the Kingdom.
Nearly half of the money in the SoftBank Vision Fund comes from Saudi Arabia and there has been a pledge of another USD45 billion this year. That gives the Saudis at least an indirect role in some of the hottest companies in the tech sector, including Uber, Slack, WeWork and Nvidia.
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