Pegg was unavailable for comment when approached last night.
His reason for including the message is still unclear, but Doctor Who fans claimed that he may have been irritated by the corporation's supposed reluctance to release a DVD of Shada, an unaired serial of the show filmed between 1979-80.
However, a spokesman for BBC Worldwide, which distributes the programme, told the Telegraph that Shada would be released on DVD and digital download next month.
They added the magazine column was "was raised with the publisher who have dismissed the writer".
It is understood that Pegg will also not be returning to his production role on the show.
Daleks on the show are operated by a separate actor, while the operator controls their movements.
Pegg had previously discussed his role in a BBC promotional video, in which he described the challenge of having to navigate the machines with "restricted visibility".
'It looks like a Dalek. It is a testament to what a fantastic piece of design it is that people just think it's a Dalek - not just a bloke and a piece of plywood," he added.
The controversy follows the recent unveiling of Jodie Whittaker as the first female Doctor to star on the show. She replaces Peter Capaldi in the latest series, which is due to air next year.