Hackers have breached security software developer, Bit9's, digital code-signing certificate through unprotected internal servers while attacking some of its customers.
The company uses a system where customers digitally sign their software to know whether the software is safe to operate on their PCs.
"As a result, a malicious third party was able to illegally gain temporary access to one of our digital code-signing certificates that they then used to illegitimately sign malware," Bit 9 Chief executive Patrick Morley said.
"There is no indication that this was the result of an issue with our product. Our investigation also shows that our product was not compromised."
The firm identified three customers who were targeted by the malicious software which had been digitally signed with untrustworthy credentials.
Customers of the security firm include the US military, intelligence agencies, five of the top 10 aerospace and defence firms in the Fortune 500, six of the top 10 petroleum refineries and three of the top 10 banks.
"The fact that this happened -- even to us -- shows that the threat from malicious actors is very real, extremely sophisticated, and that all of us must be vigilant," Morley added.
"We are confident that the steps we have taken will address this incident while preventing a similar issue from occurring again."