The company said that the issue is due to a timeout mechanism that had been left on and set to expire on August 12. This, said the company, caused the system to lock out users and believe that the license had expired.
The issue only affects systems that run ESX 3.5 Update 2 and ESXi 3.5 Update 2.
The timeout feature is often used by developers to when distributing test builds to users in order to prevent them from running and distributing test versions of the software indefinitely.
In a blog posting, VMware assured users that the issue was not a security risk, and that the cause of the problem had been found.
"Several customers have been worried that their ESX systems had been compromised by an attack and that this was the cause for not booting," the company said.
"The problem that surfaced today is not related to exploitation of a security issue on ESX."
The company said that it is in the process of producing a temporary "express patch" due to be released by 6:00 Tueday evening US pacific time.
Users can also temporarily work around the flaw by setting the system's date and time to an earlier day.
VMware hopes to have a permanent patch ready for release by noon pacific time (20:00 GMT) on Wednesday.