The revelation was included in an email sent by Clive Goodman, former royal editor at the News of the World newspaper, to the tabloid's then editor Andy Coulson, a co-defendant in the trial.
Prosecuting lawyer Andrew Edis said the March 2005 email claimed the monarch was "upset" about the officers' behaviour, as "apparently they were helping themselves to nuts".
"They were all being scoffed by police. That irritated Her Majesty apparently," Edis told the Old Bailey court in London.
Amid laughter in court, the judge joked with the jury that the suggestion that police officers were stealing nuts was "an unproven allegation".
Coulson was editor of media baron Rupert Murdoch's News of the World weekly between 2003 and 2007, and went on to work as Prime Minister David Cameron's communications chief.
He is accused of conspiring to hack phones and of conspiring with Goodman and others to commit misconduct in public office.
The trial is the first time criminal charges have been put to those accused of involvement.
The court also heard today that former News of the World news editor Ian Edmondson is no longer fit to continue standing trial on phone-hacking conspiracy charges.
"The consensus of opinion of doctors instructed both by the defence and the prosecution is that he is currently unfit," judge John Saunders told England's central criminal court.
He ruled that Edmondson, 44, should be tried by a different jury at a later date.
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