TOKYO—The operator of one of Japan’s leading trading platforms for cryptocurrencies said it lost $530 million in customer assets, the largest known crypto theft and a development that could chill the craze for bitcoin-related assets.

Coincheck Inc., a Tokyo-based cryptocurrency exchange, said Friday that 523 million units of a virtual currency called NEM disappeared due to unauthorized access by someone outside the system. It said the missing cryptocurrency all belonged to the exchange’s customers and was valued at ¥58 billion,...