There has been a series of attacks on the registries where carbon permits are stored, and EU officials announced the closure of the ETS system Wednesday after the Czech Republic-based firm Blackstone Global Ventures said about $9 million of carbon allowances appeared to have disappeared, EUobserver reported.
Thefts from electronic registries in Austria, Greece, Poland and Estonia have also been reported in recent days.
"Incidents over the last weeks have underlined the urgent need" for enhanced security measures, the EU Commission said while announcing the closure of the bloc's ETS system.
By placing a price on carbon emissions, the ETS is designed to lower company emissions and protect the environment from global warming.
Companies received emission permits for free under the first phase of the scheme from 2005 to 2007, but the EU wants to see energy companies buy all their permits from 2013 onwards.