Living For Love failed to make the station's playlist, which dictates its most-played songs, when it was released last month, leading to accusations of ageism from the 56-year-old's fans.
Speaking to The Sun, Madonna said she was 'shocked' by her exclusion. 'I was like, 'Wait a second. Shouldn't it be to do with whether you wrote a good, catchy pop song?'
Radio 1 says Madonna's age had nothing to do with its decision, saying it chooses songs on 'musical merit and their relevance to our young audience on a case-by-case basis. An artist's age is never a factor,' it said in a statement.
However, BBC News has learned that the station turned its back on Madonna long before Living For Love was released.
Speaking at a Radio Academy event last year, Radio 1's 49-year-old head of music, George Ergatoudis, said the station had 'moved on' from her music.
Ergatoudis, who chairs the weekly playlist meetings, had been asked whether he would play Madonna's next single if she agreed to appear at Radio 1's Big Weekend festival.
In response, he said: 'The BBC Trust have asked us to go after a young audience. We've got to concentrate on [people aged] 15-30. We have to bring our average age down. That's something we're very conscious of. The vast majority of people who like Madonna, who like her music now, are over 30 and frankly, we've moved on from Madonna.'
In her interview with The Sun, Madonna expressed disbelief that age would be a factor in deciding whose music to play on daytime radio.
'My manager said to me, 'If you're not in your twenties, it's hard. You might get your record played in your thirties. There's a handful of people who do - Pharrell [who is 41] got lucky. But if you're in your fifties, you can forget it'. Really? Is that how it's broken down? I'm so stupid. I didn't know it was anything to do with my age. I just do my work. We've made so many advances in other areas - civil rights, gay rights - but ageism is still an area that's taboo and not talked about and dealt with.'
Radio 1 does continue to play other artists above the age of 30 - including the Foo Fighters, whose frontman Dave Grohl is 46. 72-year-old Paul McCartney also appears on the current playlist, although only as a featured artist on Kanye West and Rihanna's song FourFiveSeconds.
The Sun has run a vocal campaign criticising the station for turning its back on artists such as Take That and Kylie Minogue.
However, Madonna's single was not completely banished by Radio 1, being played on some of its specialist shows. One of the DJs who gave the song airtime was Annie Mac, who took over the influential Evening Session programme earlier this week.
She told The Independent: 'I'm a lifelong Madonna fan and I played her on my Friday show. [Living For Love] was produced by Diplo, who is one of the biggest artists on my show. If I'm excited by a song, then I think it's going to be all right to play it.'
From BBC News