A spokesman for the independent press regulator, which is under pressure to prove it still 'has teeth' without statutory underpinning, said reports it had 'told' editors what to do were inaccurate.
Despite receiving 3,600 complaints from the public, the PCC has yet to decide whether The Sun's decision to run the pictures requires further investigation.
The PCC spokesman said it had simply issued a commonplace advisory notice, which it does 'twice a week' via email, conveying the wishes of Clarence House.
'We left it up to editors to decide whether they would publish the pictures,' he said. 'There was certainly no formal, consensual agreement that they would not be published.'
The Sun's managing editor David Dinsmore explained in an online video that the decision had not been taken lightly, but that the issue had become about 'press freedom'.
He said: 'This is about the ludicrous situation where a picture can be seen by hundreds of millions of people on the internet, but can't be seen in the nation's favourite paper.'
The PCC spokesman stressed Prince Harry's representative had not yet lodged a formal complaint.