The revelation was made at a judicial hearing by Aidan O’Neill QC, representing a cross-party group of parliamentarians headed by SNP MP Joanna Cherry and Liberal Democrat leader Jo Swinson, and immediately prompted heated reaction from anti-Brexit campaigners.
The group of MPs and peers wants Scotland’s highest civil court to rule that Mr Johnson has acted illegally and unconstitutionally by proroguing Parliament ahead of the UK leaving the EU.
The court in Edinburgh was told that Mr Johnson had declined to give a sworn statement setting out his reasons for shutting down the Westminster Parliament.
But David Johnston QC, representing the UK Government, argued that proroguing Parliament was a political decision and the courts should not be involved.
Lord Doherty, the judge presiding, heard from both sides in the case and is expected to deliver his ruling at 10am on Wednesday.
Mr O’Neill is seeking an interim interdict on the proroguing of Parliament on behalf of the parliamentarians.
But it was the discussion of a note dated 15 August from Nickki da Costa, a former director of legislative affairs at Number 10 and seen by Prime Minister Boris Johnson and his adviser Dominic Cummings, that raised most eyebrows at court number nine in Parliament Square.
The letter asked whether an approach should be made to prorogue Parliament – and a note of “yes” was written on the document, the Court of Session heard.
Mr Johnson replied the following day with a handwritten note describing the September session of Parliament as a “rigmarole” designed to show MPs were “earning their crust”. He added it should not be “shocking” to suspend Parliament.
Mr O’Neill told the court: “One presumes this is a document which was sent in the red box to the Prime Minister for him to read at his leisure in the evening of 15 August in which he says ‘yes’ to approaching the palace with a request for prorogation.”
He added: “That appears to be developing government policy as of 15 August, but this court was told nothing of that [by UK Government lawyers] and was told, in fact, that this judicial review is academic, hypothetical and premature.
“That is not true. This court and these petitioners were being actively misled.”
The Queen met the Privy Council on 28 August to approve the move, with critics such as First Minister Nicola Sturgeon branding Mr Johnson a “tin pot dictator”.
A decision was made to bring a full hearing forward to Tuesday from this Friday after Lord Doherty ruled it would be “in the interest of justice that it proceeds sooner rather than later”.
If an interim interdict had been granted, it would have immediately lifted the royal order to suspend Parliament. A full interdict could still be granted by the judge.
Responding for the UK Government, Mr Johnston said: “This is political territory and decision making which cannot be measured against legal standards, but rather only by political judgements which must permit a degree of flexibility according to circumstances.”
In a statement following the proceedings, Ms Cherry, who is leading the cross-party legal campaign, warned the secret exchange raised serious concerns over the Prime Minister’s conduct and attempt to sideline democracy to avoid scrutiny over the government’s Brexit plans.
She said: “These staggering documents disclosed in court proceedings reveal that Boris Johnson secretly agreed with his advisers to suspend parliament – before publicly denying such a move would happen.
“Rather than respecting Parliamentary scrutiny and democracy, the Tory leader is increasingly culpable of downright deception and a litany of lies.
“My cross-party legal challenge is a crucial step in holding the Tory government to account and scrutinising whether or not Boris Johnson’s decision to prorogue Parliament – which we now know was agreed back in mid-August – is unlawful and unconstitutional.
“As the lead Petitioner in the case, I have lodged a sworn affidavit and it is telling that the Prime Minister has refused to do likewise.”
A Downing Street spokesman said it was incorrect to say the Prime Minister was proroguing in order to stop MPs debating Brexit when Parliament returned.
He added: “What we are doing is bringing forward a Queen’s Speech to help the NHS, fight violent crime, AND invest in infrastructure.”