A tweet from Colfer's verified Twitter page started the rumour that the actor was quiting the show but the actor's manager and Studio 20th Century Fox Television later confirmed his account was hacked, said the Hollywood Reporter.
The actor's publicist said Colfer was on a flight without WiFi access and was not immediately available to update his Twitter account.
Studio 20th Century Fox Television also issued a statement confirming Colfer will be back for the final season.
"We've been alerted that Chris Colfer's Twitter account has been hacked. Rumors of his dismissal from Glee could not be further from the truth. We love Chris and look forward to working with him again this season," the studio said.
Colfer, 24, later took to Twitter to joke about the incident.
"Apparently I missed quite an interesting day while aboard my flight. I am just glad that I was not killed by a fruit truck again," he said referring to a previous online death hoax story.