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.
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