Company President and Chief Financial Officer Robert Baldwin Jr. disclosed the investigations during Heartland's quarterly conference call with investigators Tuesday, saying that the SEC had launched an informal inquiry into the company and that there is also a related investigation by the Department of Justice. The U.S. Department of the Treasury's Office of the Comptroller of the Currency (OCC), which regulates national banks and their service providers, has launched an inquiry, as has the FTC, he said.

Heartland has also been hit with a relating to the breach, which was publicly disclosed on Jan. 20. "We may, in the future, be subjected to other governmental inquiries and investigations," Baldwin said during the call. "We intend to vigorously defend any claims asserted against us."

Hackers were able to break into Heartland's systems and collect unencrypted data on payment card transactions that the company processed on behalf of its merchant clients. Merchants at about 250,000 locations, including retail stores, gas stations and hotels, use Heartland's services. Heartland does not know how long the hackers were able to steal credit card information or how many cards were affected.

In recent months at least three credit-card processing companies, including Heartland, have been the victims of sophisticated criminal attacks resulting in millions of compromised payment cards. One of the other card processors, RBS WorldPay, lost data on 1.5 million customers. A third hack, at an unnamed payment processor, was disclosed last week.

The Treasury's OCC may be taking an interest in the breach because it could be part of a larger problem for the banking industry, said Avivah Litan, an analyst with Gartner Research. "I think that the criminal gang that targeted Heartland is targeting multiple payment processors and it's a serious threat to the integrity of the payment systems," she said.