Panda's free antivirus, retail 2015 service, and its enterprise cloud-based antimalware service are all affected. It's not clear how many machines are affected.
The company took to Twitter to warn users: "Please, don't reboot PCs. We'll keep you posted."
In an advisory, Panda said the erroneous signature file was "repaired immediately," but warned under certain conditions it is possible for the "incident to persist."
A Panda spokesperson told ZDNet on Friday that it has fixed 90 percent of incidents. Without giving specific figures, the spokesperson said the incident affected "only a small part" of its install base.
It's not the first time an antimalware service has mistakenly classified core files as malware. In 2010, McAfee accidentally deleted a crucial Windows XP file, leaving millions of machines bricked.