A spokesman for Clarkson insisted it's nothing personal, but the stance prompted a public scolding from "American Idol" judge Simon Cowell.
"I think that by ignoring the show you're ignoring the audience who put you there," Cowell said on Tuesday.
Clarkson has become a major star in the past year, with her hit "Since U Been Gone" earning both massive sales and critical respect, particularly from a rock community that has looked upon "American Idol" contestants warily. Her album "Breakaway" earned a Grammy nomination for best pop vocal album.
Yet it may have cost her a good relationship with the nation's most popular talent show.
"American Idol" must obtain permission from owners of song licenses before the music can be used on the show. While many love the exposure, some artists — the Beatles, for one — like to rigidly control use of their music.
Clarkson is not allowing any of her songs to be licensed for other uses, said Roger Widynowski, a spokesman for Sony BMG. "It has nothing to do with 'Idol,'" he said.
The show's executive producer, Nigel Lythgoe, said he spoke to Clarkson's manager on Friday and the manager said he was unaware of the situation. He said he's waiting for a call back.
Before "Breakaway," Clarkson fired Simon Fuller, the "American Idol" creator, as her manager, saying that although he was a "great guy," she needed someone who could give her career more attention. She teamed with Swedish hitmaker Max Martin on "Since U Been Gone."
It's the same delicate position faced by countless other musicians through show biz history, wanting to break away and show artistic independence without alienating those who gave them their start.
Cowell said he hoped Clarkson would let her music be used on "American Idol."
"No matter how talented Kelly Clarkson is, she would not be in the position she's in now without winning this show," he said. "And forget the way she feels about us or the producers or anybody else, or the terrible songwriters she alleges she was with which sold her millions of records.
"It's the public who bothered to pick up the phone to vote for her," he said. "If she refuses to give songs to be used on the show, it's like saying to every person who voted for you, `you know what? Thank you. I'm not interested in you anymore.'"
With the seemingly unquenchable public interest in "American Idol," it's not like the show really needs Clarkson. But she's plainly the best example producers can point to in proving how they can open the door to wish fulfillment.
Widynowski said he would not comment on Cowell's remarks.
For his part, Cowell said, "I don't like this, when they walk away from the show and kind of forget."