Austria said last month that 488,141 permits were missing.
"In the course of the cyber attack on the Austrian emissions trading registry in the beginning of January, illegal transactions were carried out. The illegally transferred allowances have been frozen in accounts in Liechtenstein and Sweden," the registry said on its website on Monday.
"Consequently, there is no risk that these allowances are traded on the market and thus no need to publish the serial numbers of the affected allowances," it added.
Austria's public prosecution service has filed a request for the permits to be transferred back to Austria, the registry said.
Last week, the European Commission allowed five national emissions registries to reopen after freezing them for over two weeks following the theft of carbon permits worth at least 45 million euros ($60.9 million).
More national registries are expected to reopen in the coming days and weeks. Austria's registry has not reopened yet as it implements additional security measures.
The European Union's spot carbon market resumed on Friday after the suspension of trade, but it has been quiet as some exchanges remain shut and as traders fear more thefts or seek to avoid getting stuck with unidentified stolen permits still in circulation.'