We will finally leave the European Union on 31 January. Big Ben won’t toll after all, but a giant clock will be projected on to No 10. Some will celebrate; some will mourn. And the government seems to hope that we will breathe a collective sigh of relief and then move on. It’s almost as if Brexit has become a distraction, something to be got out of the way. The next five years, we are assured, will be about other things.

It’s true that Brexit may not dominate the headlines in quite the way it has done over the last few years. But even if the surface remains calm, beneath it there will be a whole lot of furious paddling. For Brexit will be the dominant driver of the underlying business of this government. Its handling of Brexit is more likely than anything else to define its legacy. A change as profound as our exit from the EU, for good or ill, entails huge and lasting consequences for this country; we are really only now, finally, at the starting gate for sorting out what that will mean.

The impact of this change will reverberate deep into government. This is without doubt the greatest challenge the British civil service has faced in a generation. The scale is vast: the negotiation of our future relationship with the EU will, in its totality, be the biggest negotiation ever undertaken by the UK. Alongside the EU deal, the government will be pushing hard to demonstrate at least one of the hoped-for opportunities of Brexit by concluding trade deals with other countries. Each trade negotiation will be a complex deal in its own right, and the interaction between any one of these and the EU negotiations will take forensic coordination, as well as hard political choices.

Brexit will require significant change to the UK legal order and regulatory state, not least as the UK civil service and UK regulatory agencies pick up the responsibilities previously managed from Brussels. The more the government wants to diverge from EU regulation, the more complex this agenda becomes.

On the economic front, new trade barriers with our major trading partner will make thousands of UK businesses less competitive in their main market. Whitehall will have to be agile and smart to work out how to counteract this drag on the government’s ambition to invigorate growth rates across the UK.

‘Whitehall will have to be agile and smart to work out how to counteract this drag on UK businesses new trade barriers will cause.’ Photograph: Alamy Stock Photo

Brexit will require a recalibration of the UK’s diplomatic outreach. Whether that’s re-establishing British credentials in international bodies such as the World Trade Organization, boosting missions in Brussels and elsewhere in the EU or adjusting our relationship with other trading partners, this will require substantial additional commitment of resources and diplomatic capital.

Within the UK itself, Brexit complicates the functioning of our own internal market, as the devolved governments take up the powers in devolved areas, such as agriculture, fisheries and the environment, that were previously managed from Brussels. Alongside the byzantine complexities of the Northern Ireland deal, Whitehall will have to re-engineer its relationship with the devolved governments to ensure the UK internal market is not compromised through the emergence of different standards on different sides of the UK’s internal borders. That will require agreement between the four governments of the UK to work together.

All this will require more civil servants – one of the unintended consequences of Brexit. There are already more than 25,000 civil servants working on Brexit, and that number will rise as we actually leave the EU. But the civil service will certainly be up for the challenge. There will be some nervousness about what lies ahead – and some disruption if the government carries through its reported plans for major changes in the way departments are structured. We know that my old department, the Department for Exiting the EU, is due for the chop at the end of the month. Handled well, this will release the brilliant capability built up in DExEU to support Brexit-related work across government. But it will be critically important to retain a sufficient cadre of DExEU officials who have deep knowledge of the EU machine and Brexit and all it entails at the centre of government to help coordinate what will be an immensely complicated negotiation with the EU.

The civil service will cope with that disruption of structural change and get on with the work it has to do. The notion that it has somehow dragged its feet on Brexit is nonsense. I know from my own experience in DExEU of the huge commitment made by thousands of civil servants across government to drive forward the mammoth task of getting us ready for Brexit. The jamming of the process through political paralysis was just as frustrating for civil servants as it was for the rest of the country.

After three and a half years of intensive engagement with Brexit, the civil service has a pretty good idea of the massive task that lies ahead. The same may not be true of many in the political class or the country more generally. Brexit done on 31 January? Yes – but only in a literal, legal sense. The truth is, we’re just getting started.

• Philip Rycroft was permanent secretary at the Department for Exiting the European Union from 2017 to 2019