Adele Green is a mother of four, who lives in the Northern suburbs of Bristol. I spoke to her last week about her son, Eddie, who is now 20 years old, and living in hospital in Doncaster, 180 miles from his family.

That may seem unbearable enough, but it pales into insignificance next to what Eddie has suffered elsewhere. Variously diagnosed with autism, dyspraxia, ADHD and more, he is now officially understood as having a learning disability with complex needs. As a child who liked cycling and dancing, and had the same caring nature he still displays, he moved through an array of educational placements before, in late 2012, he ended up at a now-defunct residential school near his home. As his mother told me last week, soon after arriving “he had a really big meltdown – it was something he couldn’t cope with, from being at home to being somewhere completely different”.

When he caused some physical damage to his immediate environment, the NHS and social care division of Bristol city council proposed that he should be sectioned under the Mental Health Act. This required the consent of his parents, who were very uncertain about whether this was the right thing to do. “But the answer was, ‘If this doesn’t happen, it could be taken out of your hands, and you could have your parental rights taken away,’” Adele told me. Because of an absence of hospital places anywhere near his home. Eddie was moved to a so-called assessment and treatment unit (ATU) in Northampton, run by St Andrew’s Healthcare – as its online blurb puts it, “a charity providing specialist mental healthcare for patients with some of the most challenging mental health needs in the UK”.

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Adele’s first phone conversation with Eddie came a couple of weeks after he was admitted. “He said: ‘I don’t like it here; they’ve got lockers.’ I said: ‘That’s absolutely fine – you can keep all your things there.’ He said: ‘No, Mum – the lockers are for me.’” What he was describing was a seclusion room: “a bare room, with no windows. Sometimes they put in a plastic mattress. There was no toilet in the one Eddie was in: he was given a bowl.”

His mother then made the first of countless weekly visits. “Eddie was brought up from downstairs as if he was a prisoner. He was so heavily sedated he couldn’t lift his head up. He’d put on stones of weight; he was dribbling. He was pale. He wasn’t Eddie.” She tells me that on all her visits she saw bruising on his body.

Even if the more terrifying aspects of Eddie’s care receded, after a spell in an NHS facility in Newcastle, he was placed in an NHS psychiatric intensive care unit (or PICU) in Salisbury, and spent six months in a so-called 136 suite, named after a section of the Mental Health Act – and what Adele calls “basically a cell”. Although his standard of care has since improved, and his family are now hopeful he will soon be living near to his family home, Eddie remains sectioned.

His is one vivid and heartbreaking story in among hundreds that form one of this country’s most awful national scandals, still lacking both public attention and any convincing action from government.

However much the language of diversity and human rights now echoes through public life, many in Britain have been left out, and remain the largely ignored victims of prejudice and abuse.

In England, there are more than 2,000 people with autism and learning disabilities in what officialspeak calls “inpatient care”. We now know about them, and the awful cruelties and indignities many of them are suffering, because of the much-maligned mainstream media – and in particular, the tireless work of the campaigning journalist Ian Birrell. Birrell and others have highlighted not just the injustice of the way very vulnerable people are treated by local authorities, the NHS and the private contractors now woven into our public services; the scandal also speaks to something that goes even deeper. It’s the fact that, however much the language of diversity and human rights now echoes through public life, many in Britain have been left out, and remain the largely ignored victims of prejudice and abuse. In different ways, people with autism and learning disabilities – two distinct categories, though about four in 10 autistic people are reckoned to satisfy the criteria for both – are still waiting for the most basic kind of emancipation. Among the many startling facts that still does not get nearly enough attention is the fact that average life expectancy for people with learning disabilities is 15 to 20 years less than the population at large.

Supposedly watershed cases of abuse inside ATUs have mounted up: 2011’s Winterbourne View scandal, and last year’s case centred on Whorlton Hall in County Durham. In 2013, Connor Sparrowhawk – who was autistic and had learning disabilities – died after having an epileptic fit in a bath at Slade House, an NHS-run ATU in Oxford. His family have campaigned for justice ever since. In late 2018, the wider story should have reached a tipping point when, even if identities and locations could not be established, Sky News discovered via freedom of information requests that 40 people with a learning disability or autism had died in ATUs over the previous two and a half years.

But somehow, the scandal drifted on. Last week the Equality and Human Rights Commission announced that it was taking legal action against the government, founded on ministers’ possible breaching of the European convention on human rights, and the fact that it has “repeatedly missed [its] targets to improve the provision of community-based care, and to decrease the number of people with learning disabilities and autism who are currently being involuntarily detained in long-term facilities against their will”.

The health and social care secretary, Matt Hancock, keeps promising to make sizeable changes but has so far failed to deliver much at all. The relevant authorities need to release much more information about cases of abuse, let alone people who have died. Basic legal injustices urgently need to be tackled: the Mental Health Act, which defines sectioning, now contains caveats for people with learning disabilities that often count for precious little at all, while no exceptions at all are made for autism, which leaves the way open to no end of abuses. There are structural stupidities in how social care is funded: if local authorities push people into the archipelago of NHS-funded mental hospitals, it relieves pressures on their finances. In turn, facilities run by private companies can maximise the revenues they get from the NHS – estimated at an average of £3,000 a week per patient – by keeping people detained at huge expense for as long as possible.

Not long after I spoke to Adele Green, I put in a call to a man called Jeremy, whose surname cannot be published. He lives in Walsall, in the West Midlands, and his campaigning on behalf of his autistic daughter, Bethany, has included defeating a gagging order attempted by his local council.

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Bethany was also held in a St Andrew’s Healthcare ATU from the age of 15. She was kept in a seclusion room, which Jeremy describes as a “cell”, in which she was fed through a hatch. The first time her father visited her, he said: “We were led past rooms of distressed people: you go down all these corridors, and at the end is a plastic window with your child behind it.” She has since begun anew in a supported living facility near Liverpool.

When I contacted St Andrew’s Healthcare for a response to Bethany and Eddie’s cases, a spokesman sent me an email in which he insisted that seclusion “is only ever used as a last resort”; that the criteria for treating someone in this way “follows the Mental Health Act code of practice guidelines”; and “we are committed to using seclusion for the shortest time possible”. Bethany’s experience of it lasted nearly two years.

Jeremy recalls that on his first visit to the St Andrew’s unit “the staff member we met was crying, saying: ‘This should not be happening.’ But that turned into: ‘This is how we are going to care for Beth.’”

Clearly the verb used in that sentence was wrong: like so many people, Bethany was the victim of a regime based not on care but on something akin to torture, and a wider system that should have long since been the subject of a huge national reckoning. The fact that it is still in place should shame us all.

• John Harris is a Guardian columnist