The prime minister was speaking after Scotland’s highest civil court ruled on Wednesday the shutdown was unlawful.
Asked whether he had lied to the monarch about his reasons for the suspension, he replied: “Absolutely not.”
He added: “The High Court in England plainly agrees with us, but the Supreme Court will have to decide.”
The power to suspend – or prorogue – Parliament lies with the Queen, who conventionally acts on the advice of the prime minister.
The current five-week suspension began in the early hours of Tuesday, and MPs are not scheduled to return until 14 October.
Labour has said it is “more important than ever” that Parliament is recalled after the government published the Yellowhammer document, an assessment of a reasonable worst-case scenario in the event of a no-deal Brexit.
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Meanwhile, the EU has said it is willing to revisit the proposal of a Northern Ireland-only backstop to break the Brexit deadlock, despite Mr Johnson ruling this out.
The President of the European Parliament, David Sassoli, said there would be no agreement without a backstop – which aims to avoid a hard Irish border after Brexit – in some form.
The Yellowhammer document – published on Wednesday after MPs forced its release – warned of food and fuel shortages in a no-deal scenario.
But Mr Johnson insisted the UK “will be ready” to leave the EU by the current 31 October deadline without an agreement “if we have to”.
“What you’re looking at here is just the sensible preparations – the worst-case scenario – that you’d expect any government to do,” he said.
“In reality we will certainly be ready for a no-deal Brexit if we have to do it and I stress again that’s not where we intend to end up.”
But shadow chancellor John McDonnell said he was “angry” that MPs would not be able to debate the planning document during the suspension.
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