The British actor became good friends with the singer after they starred together in The Next Best Thing in 2000 and provided backing vocals on her hit American Pie.
But in his 2006 memoir Red Carpets And Other Banana Skins, Rupert referred to Madonna in what appeared to be disparaging terms.
However, during an appearance on Piers Morgan’s Life Stories on Thursday, Rupert insisted he wasn’t being derogatory.
Asked by Piers what he called Madonna in his book, Rupert replied: “A screechy barmaid?”
“An old whiny barmaid,” Piers corrected him. “You didn’t finish there … You called her a curious little thing, Satan, a she-man. And you appear surprised that it put a little [cloud] over your relationship.”
Rupert then explained that he wasn’t trying to be offensive.
“The whiny old barmaid was meant to be a compliment,” he said, recalling Madge speaking in a slightly whiny voice when she was younger.
“She really got guys like that,” he explained. “And she was really charming. That wasn’t meant to be rude actually … Are you sure I put ‘old’?”
During the same episode of Life Stories, Rupert said that Colin Firth used his tongue in a kissing scene when the two shot the St. Trinian’s film.
In the 2007 comedy, Rupert plays a woman named Camilla Fritton, who ends up smooching with Colin’s character, Geoffrey Thwaites.
“The weird thing was, I had no idea that Colin was going to tongue me,” Rupert admitted.
Piers Morgan’s Life Stories airs on ITV, Thursdays at 9pm.