The revelation comes in what The Sunday Times describes as an unprecedented leak of official documents.
The classified files set out the most likely - rather than worst case scenario.
They show the UK government expects the return of a hard border to the island of Ireland.
Senior officials there believe widespread checks will be necessary as current plans to avoid them will prove "unsustainable".
The documents also show Britain will face shortages of fuel, food and medicine if it leaves the EU without a transition deal.
It comes as Boris Johnson will tell French and German leaders that there must be a new Brexit deal when he meets them next week.
The British PM is heading to Berlin on Wednesday and Paris on Thursday ahead of a G7 summit of world leaders.
However, the European Union has previously said it wouldn't renegotiate.