The police said they had not been able to prove their suspicions
There is evidence the phones of Princes William and Harry were hacked into by a News of the World reporter, a senior Metropolitan Police officer has said.
Royal reporter Clive Goodman was jailed for four months in 2007 for plotting to hack into royal aides' voicemails.
Ch Supt Philip Williams told the Commons Culture Committee the princes may also have been personally targeted.
The newspaper said it knew of "no evidence" to back the claims and that police had not mentioned them earlier.
The police had not brought up the allegations during their original investigation, a News of the World spokesman said.
In his evidence to MPs, Mr Williams acknowledged that the police had "never been able to prove" their suspicions regarding the two princes' phones.
But pressed about whether they had solid reasons to suspect the princes' personal phones had been hacked into, he replied: "Yes".
"Their voicemails may well have been intercepted," he said.
He was being quizzed, alongside Assistant Commissioner John Yates, on why police had decided not to reopen their investigation into the phone hacking scandal, after a series of stories in the Guardian in July this year reignited interest in it.
The newspaper revealed that the head of the Professional Footballers' Association, Gordon Taylor, had received £700,000 in damages and court costs last year in a case against the News of the World, but on condition that details of the case were not made public.
The police already knew about the Taylor case and Mr Yates said that from their point of view, the Guardian reports were "three old stories conflated into one" and contained no new evidence.
He was also quizzed about the apparent speed with which he had conducted a review of the evidence before deciding not to reopen the case, a decision taken over the course of a single day.
He said he had not been asked to review the evidence by Metropolitan Police Commissioner Sir Paul Stephenson, merely to "establish the facts".
He was also questioned by the MPs about an e-mail which committee chairman John Whittingdale has suggested implicates the News of the World's chief reporter Neville Thurlbeck in the phone-hacking scandal.
The e-mail contained transcripts of messages hacked into by private investigator Glenn Mulcaire, who was also jailed in 2007, from the phones of Gordon Taylor and his legal adviser, Jo Armstrong.
It was sent by a junior reporter to Mulcaire, and marked "hello, this is a transcript for Neville".
Mr Yates, who accidentally named the junior reporter in his evidence to the committee, said the decision was taken in 2006 not to question Mr Thurlbeck about the e-mail and even if he had been questioned he would probably have said "no comment".
He said there was no evidence Mr Thurlbeck had seen or read the transcript, or even that the Neville mentioned in the note was Neville Thurlbeck, arguing that it could be another Neville at the News of the World or in the "journalistic community".
Plaid Cymru MP Adam Price, who was one of a number of MPs on the committee to suggest the 2006 police investigation had been too narrowly focused, said the committee would find out how many Nevilles were working at the newspaper at the time before publishing its report.
Former News of the World editor Andy Coulson - now a key aide to Conservatives leader David Cameron - and Tom Crone, legal manager of News Group Newspapers, the News of the World's parent company - were quizzed in July by the committee about whether the princes' phones had been hacked.
Both men said they had no recollection of the story at the centre of the allegations, which was about a phone message left by Prince William imitating Chelsy Davy, his brother's then girlfriend, on Prince Harry's phone.
Mr Coulson repeated his assertion that he had not known anything about Mr Goodman's activities or those of Mulcaire.
He told MPs that he had regretted things going "badly wrong" at the paper and had taken responsibility by stepping aside.