“This was an egregious case of a clear failure to comply with generally accepted standards of behaviour of public authorities,” said one of the three judges, Lord Philip Brodie.

Last month members of the Privy Council sent by Johnson went to visit the queen at her summer castle in Balmoral to ask for the prorogation, as the suspension procedure is known.

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They claimed it was to reset the government – culminating in the Queen’s Speech – on its new domestic programme on October 14.

The parliament, where Johnson does not command a majority, took the view that Johnson wanted MPs and parliamentary select committees out of the way to stop them scrutinising his actions.

The decision from Scotland, in a case brought by more than 75 opposition MPs, comes after a preliminary court hearing in London last week found that the prorogation was political, and therefore not in the jurisdiction of the courts.

For his part, Johnson on Thursday denied misleading the queen about his reasons for suspending parliament – telling reporters the claims were “absolutely not” true.

“I’m not going to quarrel or criticise the judges,” he said. “It’s very important that we respect the independence of the judiciary. They are learned people.”

The government has appealed and the Supreme Court in London will make a final decision on whether the parliamentary shutdown was illegal on September 17.

“It is absolutely central to our constitution that the relationship between the prime minister and the queen is one of the utmost confidence and the utmost good faith,” said Dominic Grieve, a former Conservative attorney general.

Grieve is one of 21 MPs sacked by Johnson last week after they voted against the government for a motion preventing a no deal Brexit.

“The prime minister has a duty of total candour towards the queen when asking her to discharge her functions,” he said.

Grieve said if the Supreme Court agrees with the Scottish rather than the English court, then Johnson should resign.

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The Scottish court will publish the full text of its decision on Friday.

Legal commentator David Allen Green suggested that the case was likely to fail when it reached the Supreme Court, pointing out that Scottish law was different from that of England and Wales.

“That is why I and others would have put the chances of the action succeeding in London as zero. And that is why cannily the action was launched in Scotland, where judges and the law would be far more receptive,” he tweeted.

According Allen Green, one of the reasons the Scottish court ruled against the government in the case, was that there wasn’t a single civil servant prepared to put their name to a witness statement.

“Usually, when you are faced as a government with a legal challenge of bad faith, all you really need to do is put down a witness statement from a minister or a senior civil servant just explaining how the decision was made,” Allen Green told LBC Radio.

“But for some reason, a witness statement was not put in this Scottish case. That has turned out to be crucial.

“In the absence of an account by the government of why they took this decision to prorogue parliament … it became open to the Scottish judges to infer that in the absence of a positive plausible explanation, that there was a bad motive, that it was being done to stop parliamentary scrutiny.”

Johnson supporters were quick to point out the ruling could lead those who support the UK leaving the European Union questioning their faith in the country’s judicial system.

“Many Leave voters up and down the country are beginning to question the impartiality of the judges,” said energy minister and Johnson loyalist Kwasi Kwarteng.

“They’re saying why are they getting involved in politics.”

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He lost six votes in parliament in the two weeks it sat under his premiership, which included blocking his no-deal strategy and two failed attempts to call an election.

With the parliament prorogued, Johnson avoided the weekly grilling from MPs and instead took to Facebook on Wednesday to answer selected questions from the public before the UK’s departure date from the EU on October 31.

In response to a question asking if he was behaving like a totalitarian leader, Johnson said he must “respectfully disagree”.

“The Operation Yellowhammer document states that medicines and medical products are particularly vulnerable to severe extended delays in the event of a no deal Brexit – confirming our concerns as outlined in our briefing document last week,” tweeted the British Medical Association, the doctors professional body.

The document also said delays at ports could last for up to three months, and admitted increased food prices would hit the poorest sections of society hardest.

Johnson has repeatedly said he doesn’t want a “no deal” Brexit but needs to retain it as an option to get a Brexit deal through the parliament.

The EU says there have been no new proposals from Johnson on how to move forward with the negotiations that have basically stalled since Theresa May resigned and Johnson took office on July 23.

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The main sticking point is still the issue of having to resurrect a customs border between Northern Ireland, which is in the UK, and the Republic of Ireland, which will remain a member of the EU.

Johnson’s most original shot so far at solving this conundrum that many fear could reignite sectarian violence is the commissioning of a feasibility study to build a 55km bridge between Northern Ireland and Scotland.

As well as the time and the cost, that part of the sea is still peppered with unexploded ammunition from World War Two, which some experts believe would make such an engineering feat almost impossible.

As the weeks go by, Johnson is looking more and more like a lame duck staring down a constitutional barrel that could blow up at any moment.

While as Len McCluskey, leader of the UK’s largest trade union, UNITE, suggested, he probably won’t be subject to a citizen’s arrest next time he goes to Scotland, but, with the civil service union now warning the prime minister not to make its members break the law, one has to wonder how much longer has he got in Downing Street.

The opposition have denied him an election so far, but, the constitutional conundrums are almost unprecedented, bringing up issues that Allen Green said had not been discussed in constitutional texts for the past two centuries.

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Johnson has already been sacked from two jobs for lying: once in 1988 as a cub reporter on The Times when he made up a quote, and the other in 2004 from his job as a shadow arts minister, after he lied about an extramarital affair with journalist Petronella Wyatt by saying it was “complete balderdash”.

“Boris Johnson has lied to every other woman in his life, why he’d make an exception for the queen seems unlikely,” tweeted Labour MP Jess Phillips following the news from court.

If the Supreme Court decides that is indeed the case, the consequences for Johnson could be even more serious than cheating on his wife.

Additional reporting by Agence France-Presse, Reuters