At the end of February, hundreds of people packed into the artfully dilapidated surroundings of Earth, a former art deco cinema in east London, for the inaugural Late Junction festival. Over two sold-out nights, it showcased exactly the kind of programming that makes BBC Radio 3’s flagship experimental music show great: a stunning set by revived post-punk pioneers This Is Not This Heat; the fractured state-of-the-nation techno of Gazelle Twin; the first ever performance by doom-jazz troupe Pulled By Magnets; and a new project featuring singer Coby Sey and Under the Skin soundtrack composer Mica Levi.

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The festival was a wonderful celebration of a radio programme that, since its first broadcast in September 1999, has placed diverse sounds from across the globe on an unusually high-profile platform. Yet the optimism of those two nights, and the programme’s forthcoming 20th-anniversary celebrations, have been shattered by the news of the BBC’s plan to cut the show from three nights per week to a single two-hour Friday evening slot from the autumn. The cuts are part of the £800m in savings forced on the BBC by the Conservative government; Late Junction, catering to a niche audience, clearly seemed like low-hanging fruit. Yet, surely, broadcasting for audiences who aren’t catered to by the commercial sector is exactly what the BBC should be doing.

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In a statement, Radio 3 controller Alan Davey said that the changes to the schedule had been made “to make sure we continue to offer a rich mix of music and culture to existing and future audiences” – Late Junction’s raison d’être. It has recently broadcast incredible sets from its festival, an innovative, spoken-word documentary on Brixton by dub poet Roger Robinson, a set of Somalian disco, a playlist of music for plants, an in-depth interview with composer Laurie Anderson and a show devoted to bagpipe music from across the globe. The slightly woolly promise of a Late Junction replacement in the form of “a new classical music programme designed for late-night listening” summons up visions of snore-inducing Spotify playlists featuring artists like the tasteful yet bland Nils Frahm.

What makes Late Junction so exciting is its presenters’ love for their selections: the programming is never self-conscious or apologetic for its strangeness, as mainstream culture often is when it confronts the left field. In its eclectic broadcasting, jazz sits alongside throat singing, contemporary classical, odd pop, folk and noise. Crucially, this has a huge impact on the diversity of the show’s programming: artists from around the world aren’t pigeonholed into a “world music” ghetto, but treated with the same seriousness as their western peers. The music frequently intersects with social, political and environmental issues, and the programme has been instrumental in championing women in a world whose coverage was hitherto dominated by men. I would hazard a guess that Late Junction’s playlist is among the most diverse found anywhere on the BBC.

Facebook Twitter Pinterest Recents offerings include an in-depth interview with Laurie Anderson

Experimental music is under immense pressure. The much-vaunted vinyl revival benefits mainstream heritage artists over the struggling fringe. Similarly, streaming services are so weighted towards popularity that the numbers just don’t add up for those operating in the left field. These artists rely on niche programming and passionate champions such as Late Junction to get their work out there, and to survive. The BBC loves to harp on about the legacy of John Peel, his individual style and refusal to compromise. Out of anything on the network, it is Late Junction that carries the spirit of Peel into the digital age, and to reduce the programme is to betray that heritage. It is a vital part of the cultural ecosystem that helps marginalised artists get their work heard. Its transmissions feel like an auditory music festival, creating a community of musicians, record labels and fans from the UK and beyond. Late Junction, and the similarly threatened Jazz Now, are also vital programmes for the outer reaches of jazz – given that the form is currently in rude health, it seems counter-intuitive to reduce the outlets for it to thrive on the airwaves.

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Whether the decision to marginalise one of the programmes that, for me, justifies paying the BBC’s licence fee will result in the kind of petition that saved BBC 6 Music in 2010 remains to be seen; the immediate cries of disappointment on social media suggest that the decision is a vastly unpopular one. The BBC’s responsibility to the public should make it a bastion of diversity and experimentation against the homogenisation of a culture dictated by the algorithms of the big tech firms. To reduce Late Junction’s broadcasts, one might assume with a view to shutting it down entirely, would not only deprive listeners, but would also cut a vital lifeline for some of the most thrilling artists operating today. After all, the left field always ends up influencing the mainstream – who knows what far-reaching consequences this short-sighted decision might have.

• Late Junction is on BBC Radio 3.