The Lethal Weapon actor was widely reported to have made anti-Semitic remarks to a police officer when arrested for a DUI in 2006.
He was also accused of using anti-Semitic slurs such as "oven dodgers" by screenwriter Joe Eszterhas in April, a claim which Gibson has vehemently denied.
Stowe, who starred with Gibson on We Were Soldiers, came to the actor's defence when questioned about his alleged behaviour on Katie.
"He has been a very good friend to me," the Revenge star replied. "He's very tortured by what's going on. I do not believe that he's an anti-Semite in my heart of hearts. I think that he's a very complex, deep individual."
The actress went on to say that she has only ever seen Gibson as a kind and caring friend.
"I can only tell you the Mel that I know. And he was probably one of the most wonderful people on the set, ever... He's a special man," she explained.
Gibson returns to the big screen in director Robert Rodriguez's Machete Kills, opening in 2013.
Watch Madeleine Stowe defend Mel Gibson on Katie below: