British firms will face extra paperwork and checks on goods at cross-channel borders under Boris Johnson’s proposals for post-Brexit trade.

The prime minister is set to tell the EU that he is willing to accept additional checks and friction at border crossings so he can prioritise promises made on sovereignty after Britain leaves the EU.

This will be seen as a significant starting point for trade talks after 31 January with the EU, which has consistently demanded alignment on regulations in exchange for a zero tariffs and quotas – a so-called “level playing field”.

The prime minister’s official spokesman said businesses should expect to face “extra processes” and not accept anything that makes the country a “rule-taker”.

He said: “The manifesto on which the government was elected was very clear that there will be no alignment. We have always been very clear that we are leaving the EU’s customs union and single market and that means that businesses will have to prepare for life outside of these. The manifesto spelt out those two things very clearly.

“We are leaving the customs union. That means businesses will have to prepare outside of the customs union. It will inevitably mean extra processes are required on EU-UK trade.”

Johnson is due to make a speech early next week setting out plans for future trade arrangements with the EU, which he hopes to negotiate by the end of 2020. Until then, the UK follows EU rules.

For years, prospective deals with the EU were premised on “frictionless trade”, particularly under Theresa May’s premiership.

Johnson’s 2019 manifesto said there would be no political alignment with the EU and that the UK would leave the single market and customs union, thus ending the likelihood of a friction-free border.

As Whitehall prepares to leave the EU on Friday, Johnson is to meet with Department for Exiting the European Union staff to thank them for their service before the department is axed. The PM’s official spokesman said Johnson wrote to the workers before his visit.

“Some of you will have joined near the very beginning of the journey, and others more recently, but without your combined efforts we would not be where we are today,” he wrote.

Staff are to be offered jobs elsewhere in the civil service. The Brexit secretary, Stephen Barclay, will return to the backbenches and is entitled to a government payout for effectively being made redundant from his role.