TOKYO—Creditors of the collapsed Japanese bitcoin exchange Mt. Gox are on course to miss out on the recent surge in bitcoin prices. Instead, it is the exchange’s former chief executive, now on trial for embezzlement, who could turn a handsome profit.

That is because the claims by people who deposited bitcoin at Mt. Gox are calculated based on the yen value of the cryptocurrency at the beginning of Mt. Gox liquidation proceedings in April 2014. Meanwhile, Mt. Gox, which is mostly owned by a company controlled by former chief...