The British-Irish boy band was jeered by members of the audience when they stepped onstage at the New York City ceremony to accept a trophy, but they were later offered some words of support from Gaga, who urged them to ignore their critics.
Now the Bad Romance singer admits she was "really upset" by the incident as the crowd's behaviour made her feel ashamed.
She says, "It really upset me. It made me feel embarrassed for my country and for Mtv. If we were at the Grammys or the Oscars that would have never happened so I found it really disturbing.
"I don't think I'd ever be booed at the Brits. Even if everyone hated me, you would be more polite. It's rude and nasty - keep your opinions to yourself."
Gaga's pep talk was filmed by an onlooker and the footage later surfaced online, but she is adamant she had no idea she was being recorded.
She adds to Capital Fm, "I had walked out at that point and I just happened to run into them. I didn't even know that anyone could hear me or anything.
"I just genuinely wanted them to know that at least one person in the room thought that they deserved to be there because I know how I would have felt. They're really nice guys, very down to earth, sweet and handsome."