Henry Newman is Director of Open Europe.

Over the last few days the Civil Service has been dragged into Westminster’s ongoing Brexit debates. First there was the economic analysis conducted by civil servants of the impact of leaving the Customs Union, which was leaked to Buzzfeed. This then developed into a row over whether my fellow think tanker, Charles Grant (director of the Centre for European Reform), had said that the Treasury was cooking the books to make the case against leaving the Customs Union. A recording was subsequently produced which showed that Grant had not said the Treasury was fiddling the numbers. The row was significant in several ways.

What Grant did say – which is certainly true – is that the Treasury is “determined to stay in the Customs Union”. Unfortunately (for the Treasury) leaving the Customs Union is Government policy, specified in the Conservative manifesto for the June 2017 General Election, and stated publicly at various points by most senior ministers, including the Chancellor himself. There are two possible explanations for what’s going on – either Treasury officials are freelancing on policy and defying the wishes of the Chancellor, or the Chancellor is willing for his department to pursue (at least in private) a policy which contradicts the stated goal of the Government on a fundamental area of Brexit.

The row is particularly potent because the Civil Service is already in the cross-hairs because of a widespread perception that it was too partisan during the 2016 referendum campaign. In my view, it was a profound mistake for the leadership of the Civil Service to have aligned the Whitehall machine so definitively with one side in what was a divisive political campaign. To be clear: my primary issue is not that many civil servants voted remain (although there are legitimate separate questions about diversity of views amongst officials). My concern is that an objective and impartial Civil Service must be seen to be politically neutral and that this objectivity was imperilled by Whitehall’s role in the referendum.

The impression that Whitehall is aligned heavily in favour of Remain is exacerbated by comments of former permanent secretaries, such as Sir Martin Donnelly, who have attacked the Government’s Brexit policy. Former officials are allowed to express their views. But in doing so, some surely make their erstwhile Civil Service colleagues wince, and risk undermining public confidence in Whitehall.

According to Tim Shipman’s Fall Out, even the Cabinet Secretary was concerned that Whitehall had become too aligned with Remain. Shipman gives an account of Whitehall’s attempts after the referendum to model the impact of leaving the Single Market and Customs Union – the very models under discussion by Grant. Shipman says that this analysis ‘drew on the work Treasury officials had done for George Osborne during the referendum campaign’ but that ‘Jeremy Heywood ordered a rewrite of key sections for ‘more balance’’. If Heywood felt that a Government document lacked balance, why had he allowed it to be published previously?

Nonetheless, I have consistently been struck by the widespread ‘can do’ and ‘let’s get on with it’ attitude in Whitehall. I have had private conversations with many senior officials who take a very pragmatic view on Brexit – some even admit to having previously been passionate Remain supporters. There is in the Foreign Office, for example, a widespread, clear-headed understanding that the logical consequences of leaving the EU, and of the commitments made during the referendum campaign, is – say – that we start from a position of having a Canada-based trade deal, although aim for a closer relationship.

What we have seen more broadly since Theresa May lost her majority in last June’s election is a strengthening of Whitehall. The Civil Service has re-emerged as a key power player in Brexit. As the Spectator has astutely observed, the views of Jeremy Heywood, Cabinet Secretary, and Ollie Robbins, lead Brexit negotiator, are discussed inside Whitehall and in political reporting as if they are equivalent players to key Cabinet ministers. Too often they seem to be political personalities rather than advisers. I should say that both are brilliantly talented and dedicated officials, devoted to the Civil Service. But there is an inherent danger in officials being seen to have too strong a committed policy position of their own, above all if that differs from that of the Government.

It’s true that the Cabinet Secretary has always been a powerful figure in Whitehall, as have other lead officials, for example the top private secretaries in Number 10. In Thatcher’s day, getting Charles Powell onside was key for ensuring a proposal ‘landed’ well with the Prime Minister. But in today’s Whitehall, I’m too often told (by civil servants!) that major decisions on the direction of policy are shaped by civil servants. For our system to work, it must be the ministers which decide. And, as I wrote for this site on Saturday, the Government has been all too reluctant to make crucial decisions, which has left too much of a political vacuum.

Finally, this row touches on another important question: is the Civil Service ready to deliver Brexit and to rise to the challenges that leaving the EU will inevitably mean? Simply asserting that we have the best officials in the world doesn’t get anyone very far. I worked with Francis Maude in the Cabinet Office on a programme of reforms designed to improve the efficiency, efficacy, and accountability of the Civil Service. Bizarrely, some of those reforms have been abandoned or reversed by May’s Government, while in other areas the pace of progress could generously be described as soft pedalling.

Given Brexit, there’s all the more urgent a need to have a Civil Service operating at the very top of its game. So, it’s worth looking at the proposals for reform coming out of Nick Herbert’s cross-party group GovernUp. Almost everyone, on both sides of the Remain/Leave divide, agrees that Brexit is one of the biggest challenges facing the country. Of course, Whitehall is responding to Brexit, with new departments and endless new hires, but as we leave the EU we need to have a more fundamental think about how well the machinery of the Civil Service works. We need the Government to get serious about reform of the Whitehall machine.