The actor's publicist, Flo Grace, confirmed the rehab report, which first appeared on People.com.
She and Stein both declined to elaborate further.
Duchovny, 48, plays a sex-obsessed character on the Showtime series "Californication," which earned Emmy nominations for casting and cinematography. The show's second season begins Sept. 28. Showtime had no comment Thursday.
The actor appeared in the film "The X Files: I Want to Believe" earlier this summer. He has been married to actress Tea Leoni since 1997. They have two children.