Johnson was speaking to the media after Scotland's highest civil court ruled on Wednesday that the shutdown was unlawful, the BBC reported.
Asked whether he had lied to the monarch about his reasons for the suspension, he replied: "Absolutely not... The High Court in England plainly agrees with us, but the Supreme Court will have to decide."
Johnson insisted that the UK "will be ready" to leave the European Union (EU) by the current October 31 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.
"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."
The current five week suspension of Parliament, a process known as proroguing, started in the early hours of Tuesday.
MPs are not scheduled to return to Parliament until October 14, when there will be a Queen's Speech outlining Johnson's legislative plans.