The news sent cryptocurrencies tumbling, with bitcoin losing about 13 per cent, ethereum down 12 per cent and ripple nearly 20 per cent lower as traders fret over the safety of their investments.
Korea Internet & Security Agency, now carrying out the investigation with police, said only four of the country's largest exchanges are subject to the Information Security Management System certification (ISMS) requirement.
The price of Ethereum also fell 9.14 percent to reach 570,000 won and Ripple dropped 9.34 percent to 640 won. That widens Bitcoin's losses for the year to 53 percent.
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"This is 'If it can happen to A, it can happen to B and it can happen to C, ' then people panic because someone is selling", said Stephen Innes, head of Asia-Pacific trade at OANDA. "Coinrail confirmed in its statement that the exchange is fully cooperating with a police investigation into the hacking, and that trading has been suspended for now".
Japan in February carried out raids on a number of exchanges following the Coinbase hack, which exceeded the US$480 million in virtually currency stolen in 2014 from another Japanese exchange, MtGox. "It actually doesn't take a lot of money to move the market significantly".
Coinrail - one of the most popular cryptocurrency exchanges in South Korea - reported a hack on its website during the early morning hours of June 10.
Bitcoin extended losses for a third day, tumbling as much as 6% Sunday as South Korean cryptocurrency exchange Coinrail said there was a "cyber intrusion" in its system.
The Korean National Police Agency is investigating the case, an official said by phone.