Clive Goodman, 48, News of the World’s editor for issues concerning Britain’s royal family, and Glenn Mulcaire, 35, are alleged to have conspired to intercept the messages on eight occasions between January and May, London's Metropolitan Police said.
Both were released on bail and ordered to attend an August 16 court hearing.
The two were arrested yesterday, along with an unidentified 50-year-old man who was later released.
Police said their seven-month investigation began with complaints from the prince's Clarence House office about intercepted messages.
Authorities say the investigation has gone beyond Clarence House to include other public figures - though police have not provided specifics.
No comment
They say the phone intercepts may have compromised security around some public figures. Prince Charles' office has declined to comment on the case.
Anti-terrorism officers are leading the investigation, and police say they are working with phone companies in an effort to identify all those whose conversations were intercepted.
Eavesdropping is a sensitive issue for the royal family, as Charles was the victim of an embarrassing incident in 1989.
The prince and his current wife, Camilla, were recorded having an explicit phone conversation while he was still married to Princess Diana.
The Sun tabloid later published the transcripts, and ran excerpts of a conversation between Diana and a man who affectionately called her "Squidgy."
Police said they did not believe the phones of any members of the royal family had been targeted.
Legal battles
The News of the World has been tangled in several embarrassing legal battles in recent months related to its aggressive pursuit of journalistic firsts.
A jury ruled earlier this month that the newspaper libelled a Scottish politician by claiming he took drugs and visited sex clubs, and awarded him A$501,352.
In another case, prosecutors dropped an investigation linked to the newspaper's star investigative reporter when a witness testified he was paid for his story.
Roy Greenslade, a veteran media columnist, said questions would be asked about whether Goodman might have acted alone or whether the senior editors of the newspaper were aware of his alleged activities.
"If they can in some way pretend that this is a rogue reporter, they will do so of course," Greenslade said. "It puts the editor under tremendous pressure."