Thomas also directed "The Brady Bunch Movie," and produced "Can't Hardly Wait" and "Charlie's Angels."
The Hollywood Reporter said deals with the "Chipmunks" movie's writers are being finalized but Thomas is already on board to direct.
It is unclear whether "My Name is Earl" star Jason Lee, who played human lead Dave Seville in last year's mixed live-action and animated movie about a trio of crooning male chipmunks, will return for the sequel, the entertainment industry trade newspaper said.
However, Justin Long, Matthew Gray Gubler and Jesse McCartney have signed on to once again lend their voices to the iconic critter characters Alvin, Simon and Theodore.
Although the plot of the follow-up hasn't been revealed, the movie is expected to feature appearances by the Chipettes, three female chipmunk pop singers. Casting is underway for actresses to lend their voices to those characters, The Hollywood Reporter said.