TOKYO—Coincheck Inc., a Japanese cryptocurrency trading platform operator that was hacked in January, said Tuesday that it has completed compensating customers affected by the hacking and resumed some exchange services.

Coincheck, based in Tokyo, spent ¥46.3 billion ($435 million) to compensate 260,000 customers who had kept a digital currency called NEM at Coincheck. The exchange said 523 million units of NEM were stolen in a cyberattack in January.

The customers received refunds in yen at a rate of 88.549 yen per NEM, in line with earlier promises by Coincheck. That is higher than the current market rate but lower than the ¥110 value at the time of the hacking.

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A Coincheck spokeswoman said the payment in yen to the former NEM holders was begun and finished on Monday. She said the company used its own funds for the payment.

The company also resumed accepting withdrawals of selected cryptocurrencies including bitcoin on Monday. It had halted the service after the hacking, saying it wanted to make sure the system was secure. The company hasn’t resumed accepting deposits.

Some Coincheck customers expressed relief on Twitter and other social media and said they would use the refunded yen to buy cryptocurrencies again.

Still, experts warn that cryptocurrencies and the exchanges dealing in them remain vulnerable to cyberattacks. Japanese authorities are investigating the hacking at Coincheck, but they haven’t reported significant progress in identifying the hackers. Many cryptocurrencies were designed to provide a high level of anonymity to their owners.

Coincheck said it couldn’t comment on the investigation.

The company, which has described itself as Japan’s largest bitcoin exchange, has said it hopes to stay in business, but it hasn’t acquired a license from the Japanese government. The nation’s financial watchdog has told the company twice to improve its governance and controls.

Coincheck executives have said they would like the company to remain independent but wouldn’t rule out a buyout if that is the best way to survive.

Write to Takashi Mochizuki at