CEZ said it had made a claim with Czech market operator OTE but had yet to receive a response. It has also filed a criminal report.
Czech newspaper Mlada Fronta Dnes reported that the stolen permits were valued at 240 million Czech crowns US $13.
6 million. CEZ declined to confirm the report pending an investigation.
"We believe the entire situation will soon be resolved," CEZ said in a statement. "In view of the ongoing investigation though, we are not going to disclose any further details."
The Czech carbon registry closed for an indefinite period after data of account holders was manipulated and EU allowances vanished.
The European Union froze spot trading in the carbon market after the security breach, which saw the theft of at least 7 million euros US $9.6 million of emissions permits from the Czech Republic's carbon registry.