Swedish Prime Minister Fredrik Reinfeldt said the British rock band had made "a monumental contribution ... and captured the mood and spirit of a whole generation in their reflections and attitudes."
The audience gave the prize winners a standing ovation when they arrived to receive the awards, each worth $157,700. The ceremony was held in the Stockholm Concert Hall.
Fleming thanked organizers for drawing attention to the importance of culture in everyday life and paid tribute to Swedish opera singers.
A two-time Grammy winner, Fleming, 49, has performed on international stages since her debut more than 20 years ago.
Pink Floyd, founded in the early 1960s, reached critical acclaim and popularity with albums such as "Ummagumma," "The Dark Side of the Moon" and "The Wall."
Mason, 63, said the band was honored to receive the award and that fellow band members David Gilmour and Richard Wright were sorry they couldn't attend.
Waters, 65, paid tribute to his 96-year old mother. "If there is any humanity and empathy in my work, which I think there is, I would rather owe it to her," he said.
Swedish artists performed the band's songs at the ceremony, ending with a sing-along to the hit "Another Brick in the Wall."
Reinfeldt recalled playing the song which has the lyric, "we don't need no education" on his school's loudspeakers when he was 14.
The Polar Music Prize is Sweden's biggest music prize and is usually split between pop artists and classical musicians. It was founded in 1989 by Stig Anderson, manager of Swedish pop group ABBA. Past winners include Paul McCartney, Isaac Stern, Bruce Springsteen, Pierre Boulez and Quincy Jones.
The 2007 award went to jazz saxophonist Sonny Rollins and composer Steve Reich.
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