Anti-terrorist police officers are also examining dozens of other mobile telephone numbers, including those belonging to a senior government minister and several celebrities.
Clive Goodman, 48, the News of the World's royal editor, was charged on one count of conspiring to intercept voicemail messages on or before 8 August this year, and eight counts of intercepting messages between January and May this year. He was jointly charged with Glen Mulcaire, 35, of Sutton, south London.
If convicted, the maximum sentence they face is two years in jail and an unlimited fine. Both have been released on police bail to appear at Horseferry Road magistrates' court on 16 August.
The men are accused of ringing the mobile phones of Prince Charles's staff and retrieving messages left on their voicemail.
An investigation by officers from Scotland Yard's anti-terrorist branch was started in December last year after a complaint by Clarence House, the official residence of Prince Charles, his wife, the Duchess of Cornwall, and the Princes William and Harry.
At least one cabinet minister, but not the Prime Minister, is understood to have been among those alleged affected along with high-profile celebrities, top footballers and other senior politicians. Police are also checking the mobile phone of Max Clifford, the publicity consultant.
It is relatively simple to hack into someone's mobile telephone message service by simply calling up their voicemail and using what is called a "default" code. Unless the phone owner installs their own code, the handset will release voicemail messages when someone uses a well-known four digit number - the automatic default option. Most people do not bother to use a code, or are unaware that they need one.
The secret affair between the former England football team manager Sven Göran Eriksson and the television presenter Ulrika Jonsson is believed to have been uncovered via that method. David Blunkett, the former Home Secretary, is convinced he was a victim of the trick when his relationship with the publisher Kimberly Quinn was revealed.
Mr Goodman, the Sunday newspaper's long-standing royal editor, was arrested at his home in Putney on Tuesday and was questioned at Charing Cross police station before being charged. Mr Mulcaire, arrested at his home in Sutton, was held at a different police station. A third man, aged 50, was arrested in Sutton on Tuesday and was released on police bail yesterday morning. All three were held under Section 1 of the Regulation of Investigatory Powers Act 2000.
Detectives are analysing a large number of telephone numbers, who they belonged to and whether they had been subject to interception. The allegations do not relate to the tapping of live telephone calls.
They have searched a number of addresses, including the offices of News International in Wapping, east London, as well as in Sutton and Chelsea.
Sources denied that phones used by Prince Charles or the Duchess of Cornwall were among those allegedly hacked into.
The chairman of the Press Complaints Commission, Sir Christopher Meyer, said: "The Press Complaints Commission sets out in clause 10 of its code of practice that the press must not intercept private or mobile telephone calls, messages or e-mails and a whole bunch of other things which come under the heading of clandestine devices and subterfuge.
"You have to have a very high bar of public interest to justify this and so that's enshrined in our constitution."
There is considerable sensitivity within the Royal Family over phone interceptions following the infamous "Squidgygate" episode in the 1990s, when details of an intimate telephone conversation between Diana, Princess of Wales, and her friend James Gilbey were published.
The Prince of Wales and Camilla were also the unwitting subjects of phone interception in 1993 when a tape of an intimate late-night phone call between them was made public in the so-called Camillagate affair.
The 'dark art' that editors don't want to know about
A former reporter on a red-top newspaper writes...
When people hear about phone taps, they often think there's a spy outside in a workman's tent. The fact is that landline tapping is very difficult to do and generally it's only the security services and sometimes the police that get away with it.
It's much harder than it used to be. There used to be default settings on the networks and some unscrupulous phone company people told journalists what they were. If people hadn't put their own code on, you simply put in the default code and got hold of their messages. In the late 1990s, around 50 per cent of exposés of celebrities were done through phone screwing.
Then networks took the default settings out and celebrities added extra security.
You could also get a complete itemised bill until a few months ago, when the Information Commissioner threatened custodial sentences. The work was all outsourced and there was one firm that was probably making £8,000 a week. It became a basic check. If two people not meant to be linked call one another 20 times, particularly at 3am in the morning, explain that to your wife.
Papers have their "dark arts" reporters and many editors don't want to know, but what was a flood of stories stood up this way is now a trickle.
There's no way you'd screw Prince Charles's or Camilla's phone - Special Branch would be on you like a ton of bricks. People who did all this stuff were generally people without many contacts. Journalism is always better if you start with a contact tip-off and then stand it up. If you listen to a phone message it doesn't necessarily tell the whole story.
Paying people for their stories will become more important now and picture prices are going to go up. Everyone else will have a moratorium on phone screwing and say, "leave it alone", but three months later it will filter back in.
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