The UK will face a three-month meltdown at its ports, a hard Irish border and shortages of food and medicine if it leaves the EU without a deal, according to government documents on Operation Yellowhammer.

The documents predict severe extended delays to medicine supplies and shortages of some fresh foods combined with price rises as a likely scenario if the UK leaves without a withdrawal agreement, which is due to happen on 31 October.

They suggest there has been a worsening of the risk since documents leaked to the Guardian showed some of the government’s “reasonable worst-case scenarios” (RWCS) involved risk to medicine supplies and disruption to food chains.

The dossier, compiled this month, says up to 85% of lorries using the main channel crossings “may not be ready” for French customs and could face queues of two and a half days, the Sunday Times reported.

Medical supplies will be “vulnerable to severe extended delays” as three-quarters of the UK’s medicines enter the country via the main Channel crossings, and the availability of fresh food will be reduced and prices will rise, which could hit “vulnerable groups”.

The government also believes the return of a hard border between Ireland and Northern Ireland would be likely as current plans to avoid widespread checks would prove unsustainable.

A senior Whitehall source told the Sunday Times: “This is not Project Fear, this is the most realistic assessment of what the public face with no deal. These are likely, basic, reasonable scenarios – not the worst case.”

Downing Street sources would not comment on the record about the leaked document but hit back at its accuracy, saying it was prepared under Theresa May’s administration and did not reflect the level of planning that had gone on under Boris Johnson.

A No 10 source said: “This document is from when ministers were blocking what needed to be done to get ready to leave and the funds were not available. It has been deliberately leaked by a former minister in an attempt to influence discussions with EU leaders.

“Those obstructing preparation are no longer in government, £2bn of extra funding has already been made available and Whitehall has been stood up to actually do the work through the daily ministerial meetings. The entire posture of government has changed.”

Leading pro-Brexit MPs also rejected the predictions made in the document. Two Tory former cabinet ministers, Iain Duncan Smith and Owen Paterson, claimed the leak was an example of an “establishment” plot to “sow fear in people’s minds”.

On Sky’s Sophy Ridge on Sunday programme, Kwasi Kwarteng, a minister at the Department for Business, Energy and Industrial Strategy, said there was “a lot of scaremongering around and a lot of people are playing into Project Fear and all the rest of it”.

Johnson insists he still wants the UK to leave with a deal but he has demanded a fresh agreement with the EU without the backstop, a mechanism to prevent a hard border in Ireland that could keep Britain in a customs union.

He is due to visit Angela Merkel, the German chancellor, and Emmanuel Macron, the French president, before a G7 summit this week to underline his demands for concessions. However, the EU is adamant that the backstop must stay.

With the likelihood of no deal increasing, more than 100 MPs from across the political parties have called on Johnson to recall parliament to allow for debate on Brexit.

Moves are under way by Tory rebels along with Labour, SNP, Liberal Democrat and other MPs to legislate against no deal. If that fails they are working on replacing Johnson with a caretaker government after a vote of no confidence.

Johnson’s strategy is to blame parliamentarians for blocking Brexit, before a possible general election that he would fight on a “people versus parliament” platform.

In a letter leaked to the Mail on Sunday, Johnson said it was “plain as a pikestaff” that EU leaders would “simply not compromise” and agree to a new deal if Tory MPs openly discussed stopping a no-deal Brexit on 31 October.

The letter will be seen as an attack on Philip Hammond, the former chancellor, and Dominic Grieve, the former attorney general, who are among those leading Tory rebels trying to find ways to stop the government leaving the EU without an agreement.

In a letter to 20 Tories who had written to him demanding a deal, Johnson replied: “Any such parliamentary campaign, any tricks of procedure or alliance of factions designed to derail Brexit, gravely damages the chances of our securing a deal.”

The government is applying its energies to showing the EU that it is serious about leaving on 31 October with or without a deal. This weekend Steve Barclay, the Brexit secretary, moved to sign a commencement order, which would trigger the end of the supremacy of EU law in the UK on 31 October.