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.
Bitcoin was one of those affected, falling 10 percent to its lowest price in two months.
The world's most valuable digital currency is now trading at $7,229 per coin, widening losses for the year to 48%. At the height of the global crypto-mania in early January, they were worth about $830 billion.
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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", Innes said.
Enthusiasm for virtual currencies has waned partly due to a string of cyber heists, including the almost $500 million theft from Japanese exchange Coincheck Inc.in late January.
Coinrail said hackers stole cryptocurrencies including Pundi X, Aston and NPER. "70% of total coin and token reserves have been confirmed to be safely stored and moved to a cold wallet [not directly connected to the internet]".
In January 2018 some $500-worth of cryptocurrency was stolen as a result of a hack on Japan-based exchange Coincheck, which led to a severe drop in market prices for various digital currencies and toughening of the country's policies towards cryptocurrency exchanges.
The Korean National Police Agency is investigating the case, an official said by phone.