Cameron was caught on camera on Tuesday making the remarks to former New York mayor Michael Bloomberg in the United States, where he was attending the UN General Assembly, in what monarchy watchers have called a breach of protocol.
"The definition of relief is being the prime minister of the United Kingdom and ringing the queen and saying: 'It's alright, it's OK.' That was something," Cameron said. "She purred down the line."
"It was a private conversation, but clearly a private conversation that I shouldn't have had and won't have again," he told reporters in New York.
"My office has already been in touch with the palace to make that clear and I will do so as well."
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By constitutional convention, the queen must remain impartial over political issues such as the Scottish independence debate and any discussions between the executive branch and the sovereign must remain confidential.
"I think it's a major blunder..., particularly embarrassing because he was speaking about a sensitive and divisive political issue," Flynn said.
The queen is kept up to date on affairs of state at weekly audiences with the prime minister and has so far met with 12 British leaders during her 62-year reign.
She reportedly had a difficult relationship with Margaret Thatcher because the late leader "would not listen," but leaks from these private meetings are rare.
Royal officials had insisted the queen would not seek to influence last Thursday's closely-fought referendum.
"Any suggestion that the queen would wish to influence the outcome of the current referendum campaign is categorically wrong. Her Majesty is simply of the view this is a matter for the people of Scotland," a spokesman for Buckingham Palace said during the campaign.