The photos, by renowned photographer Annie Leibovitz, were taken to accompany an interview with the 15-year-old pop star and her father, singer Billy Ray Cyrus. They include shots of the teen reportedly topless and wrapped in a blanket.
The Disney Channel, which airs Cyrus' TV show "Hannah Montana," was also critical of Vanity Fair.
"Unfortunately, as the article suggests, a situation was created to deliberately manipulate a 15-year-old in order to sell magazines," a network statement said.
A phone message left for a Vanity Fair representative was not immediately returned Sunday night. But in a statement to the TV show "Entertainment Tonight," Vanity Fair defended its position.
"Miley's parents and/or minders were on the set all day," the magazine said. "Since the photo was taken digitally, they saw it on the shoot and everyone thought it was a beautiful and natural portrait of Miley."
Cyrus is one of the biggest - and most G-rated - acts in the country and is often considered a role model for young girls.
Her "Best of Both Worlds" tour sold out arenas, and her successful 3-D concert film collected $31.3 million in its opening weekend in February.
