The producer has claimed that the screenplay that has been circulating online is an old draft from before he became involved with the project.
"The leaked script for Ninja Turtles that different sites continue to comment on was written well before I, or anyone at Platinum Dunes, was involved with the project," Bay wrote on his official website's forums.
"That script saw the shredder a long time ago. This is tired, old news - wait for the movie!"
The leaked screenplay has caused amusement and concern among fans since it appeared last month.
Ninja Turtles co-creator Peter Laird has labeled the script as a "wretched thing".
Bay has already caused controversy by deciding to reboot the Turtles as aliens.
The release of Ninja Turtles has been delayed until May 2014.
Watch a 1990s Teenage Mutant Ninja Turtles movie trailer below: