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The writer is a senior fellow at the Institute for Government think-tank

In a welter of jaw-dropping statements revealed by the Covid inquiry, perhaps the most surprising so far has been a WhatsApp from the cabinet secretary, Simon Case. “Government isn’t actually that hard,” wrote the man who served Boris Johnson during the crisis and is still in his post as most senior civil servant in the UK. He did go on to point out that Johnson was still not up to it, but his having this thought at all should be a source of concern.

Case is wrong. Government is hard. The inquiry has shone light on the ways in which it was easier for both ministers and civil servants to take comfort in a plan without asking whether it was up to scratch. How easy it was to think about the impact on services without taking into account the impact on people. How quantifiable economic impacts are easier to handle than diffuse unmeasurable social consequences that have no one to speak up about them inside government.

And government is much, much harder when it is conducted in a sulphurous atmosphere of contempt and recrimination. The inquiry has lifted the lid on the “toxic” environment at the centre of government, where special advisers think civil servants are useless, civil servants think advisers are “feral” and special advisers and civil servants agree that their political masters are “useless”, “mad” or “trolleys”.

It will be all too easy to conclude that the big lesson from the inquiry is that when the pandemic hit we had the wrong prime minister (and the wrong health secretary for that matter) to cope with a crisis of this magnitude. But it is also becoming clear that the UK response was hampered by longer-running problems in the civil service and the way we organise government.

Covid blindsided an inexperienced government led by a gifted campaigner, not a diligent administrator, with ministers largely selected for their Brexit views not their competence, and a civil service drained by four years of mayhem after the vote to leave the EU. The latter was led first by someone who had been diminished by repeated clashes with the prime minister; then by Case, an allegedly reluctant prime ministerial appointee who, it has now emerged, had already lost confidence in Johnson.

Ministerial frustration with the civil service did not begin with Brexit. Margaret Thatcher complained of what her successors would describe as a “blob”; when she suspected civil servants of not being “one of us”, she meant not supporting her agenda. Even mild-mannered Geoffrey Howe marginalised his inconvenient permanent secretary at the Treasury. Tony Blair complained of the impossibility of public sector reform. Sir Iain Duncan Smith’s advisers blamed officials for the troubled implementation of universal credit. Permanent secretaries who fell out with their political masters were discreetly found a berth outside government.

But Brexit made relations more difficult and more overtly hostile. Although some ministers acknowledged the work their civil servants did to get it over the line, others were suspicious of those they saw as natural Remainers. David Davis doubted any permanent secretary would have supported Brexit. Forecasts that suggested Brexit would damage the economy or new trade deals disappoint were denigrated. Theresa May’s lead Brexit negotiator, Sir Oliver Robbins, was a lightning rod for ire at compromises in her withdrawal agreement — it was easy for internal party foes and Faragist outriders alike to paint her as the puppet of a civil service that wanted to soften Brexit.

Dominic Cummings, architect of the Leave campaign’s victory, saw Brexit as a means to shake up the establishment in general and the civil service in particular. In her evidence to the inquiry, deputy cabinet secretary Helen MacNamara noted that in February 2020, rather than focus on the pandemic, top civil servants were “distracted” by trying to shelter from Cummings’ promised “hard rain”. They were right to worry; it washed away seven permanent secretaries, including the cabinet secretary who preceded Case, Mark Sedwill.

Case and Sedwill described Team Johnson as “wild animals”. MacNamara was hounded out of her job that year when as head of propriety and ethics she crossed swords with Johnson and Cummings — ministers clashed with civil servants trying to uphold norms that had previously been well understood.

So Covid was managed by ministers, civil servants and special advisers with little trust in each other or even each other’s abilities. The inquiry will have the final verdict on how much that affected the pandemic response but, at a minimum, it seems much time and effort had to be devoted to managing a capricious and unserious prime minister and a mendacious health secretary. Good people avoided key roles: they feared “being shot in the back”.

Meanwhile, real shortcomings in the civil service are being exposed, which leadership needs to address, from data illiteracy and longstanding weaknesses in scientific understanding to wider issues such as contingency planning, compounded by complacency. There was a lack of empathy or understanding about how measures might affect people’s lives. Future cabinet secretaries — it may be too late for Case — need to cut the banter and insults and once again become figures who can command authority among ministers and officials.

But ministers have a critical lesson too: they must allow space for constructive challenge from civil servants before things go badly wrong.

And if relations have deteriorated too far, it might be time to reset, to put more clarity on respective responsibilities and, perhaps, more formal distance between ministers and civil servants.

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