A spokeswoman for St James's Palace said it was disappointed that the newspaper had decided to publish the pictures of the prince at school.
The unauthorised pictures in Sunday's edition show the prince playing football and polo, going for a run at Eton and talking to friends.
A spokeswoman for St James's Palace said it was disappointed that the newspaper had decided to publish the pictures of the prince at school.
The palace said in a statement: "We will be taking the matter of current media coverage of Prince William up with the Press Complaints Commission (PCC) this week and asking the PCC to give further consideration to the issues involved before it sets out guidelines on the privacy of Prince William after he leaves school.
"The privacy of Prince William and Prince Harry at school has always been of paramount importance to us and it is vital for us to reaffirm the principle that the two young princes, like all children, should be free to complete their time at school without interruption.
"This is of continuing importance to us because even though Prince William himself will shortly be leaving school, Prince Harry remains at Eton."
An authorised set of photographs to mark Prince William's 18th birthday are scheduled to be published next Saturday.
But the publication of those pictures has also provoked controversy, with a dispute between St James's Palace and the Daily Telegraph over ownership of the photos.
Sandy Henney, who had been the Prince of Wales' press secretary for seven years, resigned over the copyright issue.
It also led to the cancellation of a speech by Lord Wakeham, chairman of the PCC, appealing for continued media restraint to guard Prince William's privacy.