Cruise says he didn't intend to come across as arrogant when he criticized Brooke Shields for taking anti-depressants in 2005.
The conversation grew heated when the star told Lauer he was glib and didn't know about psychiatry.
Cruise, who has been a Scientologist for 25 years, agrees with the religion's long-running campaign against psychiatry and the pharmaceutical industry.
The mea culpa comes as Cruise is making rounds on talk-shows to promote his new movie, "Valkyrie."
Cruise stars as a would-be assassin of Adolf Hitler in "Valkyrie," which is to be released Dec. 25.