In the last two weeks, three damning reports have been published by the chief inspector of prisons. Doncaster is failing, Hindley is failing, Isis is failing. The litany of disasters is seemingly endless: children found hanging in their cells, prisoners attacked with make-shift weapons, stuffed in a cell together, locked in 23-hours a day, staff numbers slashed, funding cut, ever more inmates being crammed into a creaking system which is coming apart at the seams.

The prison estate is very good at preventing prisoners, or former prisoners, from talking to journalists. But the reports which do come in mention unreported protests by inmates after being locked up all day, small-scale riots and a fundamental breakdown of trust between inmates and guards.

I'm told that one prison has started transporting sex offenders to other facilities. Sex offenders are usually the first victim of prison disorder. Their removal often indicates that authorities are losing confidence in their ability to control an institution.

For the first time, the justice secretary deigned to talk about it yesterday on the Today programme, if only to deny there was any crisis. His only other pronouncements are becoming increasingly paranoid, as if he is imagining ever-more villainous enemies among the people who point out the failings in the system.

A week ago, an article by Grayling attacking charities went up on the Telegraph website and then was immediately taken down. Perhaps the editorial staff thought twice at publishing a piece which appeared to show an author balanced perilously on the edge of political rationality, even if he is a secretary of state.

It went up again over the weekend. It is a quite deranged piece of writing, not improved by the Telegraph's strange style-guide insistence on capitalising the term 'Left', as if this were a missive from Trotsky.

Grayling says the internet petition site 38 Degrees is "in name, a forum for people to start their own campaigns, but in reality, an anti-government pressure group".

He goes on: "As with much of the Left's campaigns and propaganda, the aim is often to portray the government in a very different light to the actual reality."

The article shows Grayling start to dwell on the idea of a fifth column, an army of Labour insiders embedded in the charity sector, intent on overthrowing the government. "The issues they latch onto are usually about spending more of your money – or undermining the crucial work we are doing to turn the country round," he warns.

He then launches into an extraordinary personal attack on Frances Crook, the chief executive of the Howard League for Penal Reform, who he calls "one of the most prominent Labour-supporting pressure group leaders".

Grayling has long detested the Howard League. He is understood to have cancelled an inquiry into sex and rape in prison because of their involvement. He stormed out of a parliamentary meeting because they were mentioned in glowing terms.

This is Crook's account of what she did over the weekend, while Grayling was writing up an attack on her. You can decide for yourself if she sounds like a Labour militant.

"Today Labour held a summit on the crisis in prisons and I was invited to attend. I decided in the end it was not appropriate as the Labour press office sent out a note pre-empting the discussion by listing the policies the party had already decided on, many of which I think are wrong or trivial. Secondly the event was branded as so partisan that I felt it was inappropriate for a charity to attend."

The Howard League is independent, impartial and non-aligned. It is funded from multiple sources and doesn't accept government grants. Grayling's attack on it is indicative of his own mindset rather than its own. He sees party political conspiracy where there is public research. He sees anti-government agitation where there is scrutiny. He is a tiny tyrant, jealously guarding his little empire as it crumbles to dust.

He's been this way for some time. I'm told that as employment minister he took to calling the Citizen's Advice chief executive every time she said anything critical about welfare reform. Sources say this eventually had some effect and led to a watering down of its criticism of the government. Gradually policy officers were stripped of their external roles, such as talking to the media.

In late 2012, the chief executive was sent a letter from Grayling in which he complained about a certain piece of work they'd done. Management told staff that the letter said: "You are a bunch of lefties, and if it were up to me I would shut you down". At that point management went into a flap and policy work was basically dismantled, in favour of a more 'think tank' approach.

Citizen's Advice, it should be said, deny they've watered down their criticism of the government and pointed me towards recent campaigns on employment support allowance as evidence they're still robust in their relationship to government.

This treatment of charities is standard operating procedure for the coalition government. It has tried to shut down charity criticism in two ways: through legislation and co-option.

The first took the form of the lobbying bill, which did nothing to address lobbying but severely hampered charities' and trade unions' role in civic society. It was so bad it united the Taxpayers' Alliance and the Trade Union Congress. Quite the achievement.

It aimed to limit spending on campaign activity in the year ahead of a general election and redefined electoral activity as anything which could affect the outcome of an election. It was a startling and undemocratic attempt to close down scrutiny, while cynically pretending to tackle lobbying.

The other method used to close down criticism from charities is incorporate them into the public service delivery system. Big, important groups with name-recognition have been hollowed out of their principles in the desperate bid for government contracts. They are terrified of commenting on government policies which are demonstrably counter to the goals they strive for.

This goes for some charities working within prisons, who are as aggressive in fielding questions about what goes on there as the Ministry of Justice. And it goes on in the realm of immigration too, where charities' role picking up the breadcrumbs left over from contracts to the likes of Serco and G4S have made them terrified of biting the hand that feeds them.

Charity criticism is being shut down in the courts and in public service delivery contracts. And when that doesn't work it is shut down by a campaign of bullying and intimidation from ministers.

Grayling's paranoid delusions are not just personal failings. They are reflections of government policy.

The repercussions are plain to see. A prison crisis has developed which no-one is trying to address. Yesterday, the chair of the Criminal Law Solicitors Association said the secretary of state and lord chancellor was "in a state of unparalleled denial". He added: "His programme has no grounding in reality. He has shown blatant disregard for the views of experts and practitioners on almost every issue. Make no mistake, this crisis is not one of prisons but of the entire English justice system."

At some point the secretary of state's refusal to listen to evidence and personal attacks on his critics must be considered more than personal failings. They are political negligence.