In an email to staff, Mr Musk said an unnamed employee made unspecified coding changes to its manufacturing operating system and sent sensitive data to unnamed third parties.
"The full extent of his actions are not yet clear, but what he has admitted to so far is pretty bad", Musk wrote, adding that the unnamed employee supposedly took action against the company after being passed up for a promotion. His stated motivation is that he wanted a promotion that he did not receive.
Company spokeswoman Gina Antonini declined to comment on the email.
Understandably, Musk suspects "there may be considerably more to this situation than meets the eye", considering that there are "a long list of organizations that want Tesla to die". "If they're willing to cheat so much about emissions, maybe they're willing to cheat in other ways?" he wrote.
Last week, Musk announced that 9% of the company's workforce was being laid off, without specifying an exact number.
The leaked emails come as Musk has been acting increasingly erratically, aggressively going after the media on Twitter, as well as investors who have been betting against Tesla.
Musk said the reorganisation did not affect hourly-paid assembly-line employees and was not expected to delay manufacturing targets. Tesla told CNBC it "was extinguished in a matter of seconds" and "there were no injuries or significant equipment damage".
Musk went on to urge employees to be "extremely vigilant" and to report anything suspicious. Musk said the fire could just be a "random event", but quoted businessman and engineer Andrew Grove's famous line that "only the paranoid survive".
Tesla's billionaire CEO Elon Musk has warned staff that there might be a saboteur in their ranks responsible for a factory fire, changing code and sending secrets outside the organisation. In the lawsuit, Tesla said the email was part of an oil-industry effort to undermine the company's push for energy-efficient transportation.