Johnson asked the British head of state to shutter parliament for five weeks from last Tuesday, claiming it was necessary ahead of rolling out a new domestic agenda.
The unusually long suspension -- known as prorogation -- was widely seen as a bid to thwart opposition to a no-deal departure on the October 31 Brexit date, and provoked uproar across the political spectrum as well as legal challenges.
Asked if he had misled Queen Elizabeth over his motives for the suspension, which will see the House of Commons closed until October 14, Johnson said, "Absolutely not".
Meanwhile, in Brussels, EU chief Brexit negotiator Michel Barnier said there was "no reason to be optimistic" about striking a possible divorce deal with Britain before a summit next month.
Johnson is adamant that the UK must leave the European Union on October 31 -- with or without a withdrawal agreement to smooth over the separation.
"We have no reason to be optimistic" that such an accord will be found in time for the crucial October 17-18 EU summit, Barnier told senior MEPs in Brussels.
Problems are mounting for Johnson, who finds himself increasingly boxed in on Brexit.
Johnson's government was forced Wednesday to release its no-deal Brexit contingency plans after a parliamentary vote.
Scotland's highest civil court on Wednesday sided with critics of the prorogation, ruling it was "unlawful" and intended to "stymie parliament".
Johnson's government has appealed against the decision and the case is set to be heard in Britain's Supreme Court next Tuesday.
In the meantime, parliament remains suspended.
Northern Ireland's High Court on Thursday dismissed several lawsuits filed there arguing the prorogation was illegal and that a no-deal Brexit would breach the terms of the province's 1998 peace accord.
Tom Brake, Brexit spokesman for the pro-EU opposition Liberal Democrats, said the government was withholding internal documents, messages and emails about the decision to prorogue parliament.
"I suspect that those documents... will confirm that the prime minister lied about the reason why," he told AFP.
"We all know that the reason he wanted to shut down parliament is because he didn't want parliament holding him to account."
Johnson also vowed Thursday that Britain will be ready for a no-deal departure from the EU on October 31, despite his own government's assessment that planning remained "at a low level".
The prime minister insisted the government had been "massively accelerating" its preparations since the August 2 internal report, which was disclosed on Wednesday after MPs voted for its release.
He called the "Operation Yellowhammer" forecast, which warned of possible civil unrest and shortages of food and medicines following no deal, a "worst-case scenario".
"All the industries that matter will be ready for a no-deal Brexit," Johnson said.
The documents painted a grim picture of possible "public disorder and community tensions" as well as logjams at Channel ports, threatening supplies, after a no-deal departure.
Johnson hopeful of deal
Johnson took office in July promising to implement the referendum decision by leaving the EU on October 31 no matter what.
But he lost his parliamentary majority last week after a series of defections and expulsions from his governing Conservative Party amid opposition to his strident Brexit stance.
Ahead of the shutdown, lawmakers passed a law aimed at preventing a no-deal Brexit, but Johnson has insisted Britain will still depart the EU on schedule.
The British leader wants to renegotiate the divorce terms struck by his predecessor Theresa May, which MPs have repeatedly rejected.
In particular, he wants to change the so-called backstop provisions, which concern ways to keep the Northern Irish border with the Republic of Ireland open in all scenarios.
But European leaders accuse him of offering no viable alternatives.
Officials in Brussels increasingly accuse Johnson of conducting a sham negotiation as political cover while planning to crash out without an accord.
And European parliamentary leaders insisted Thursday there could be no divorce deal without the backstop.
Johnson insisted he remained "very hopeful" of a deal.
"It will be hard, but I think we can get there," he said.
Asked if he had misled Queen Elizabeth over his motives for the suspension, which will see the House of Commons closed until October 14, Johnson said, 'Absolutely not'