Coinrail said hackers stole cryptocurrencies over the weekend including Pundi X, Aston and NPER. It did not give a value but Yonhap News agency cited unnamed industry sources saying coins worth about 40 billion won (£27.7 million) were lost.
If true, that would make it the biggest cryptocurrency theft reported to date in South Korea.
Bitcoin was trading at $6,780 (£5,050) on Monday, down from more than $7,500 (£5,586) before the weekend, according to Coindesk, which monitors prices.
Coinrail said it was cooperating with police and suspended trading. News reports said Coinrail, launched in September, was the seventh-largest exchange in South Korea by trading volume.
South Korea has seen a craze over bitcoin and other cryptocurrencies, prompting authorities to try to rein in speculative investment this year by tightening regulations. Cryptocurrencies are still popular, especially with young investors.
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