Harry and Meghan had to leave their home after the pictures were published in stores, including The Times magazine, a royal source familiar with the story told CNN.
Splash News chartered a helicopter in January to take pictures of the couple's private home in the Cotswolds region of England, which Buckingham Palace said the couple's security is in danger.
"Syndication and publication of the photographs severely undermined Duke's security and home to the extent that they can no longer live on the property, the palace says in a statement.
"The helicopter flew over the home at low altitude and allows Splash to take pictures in and out of the living room and dining room of the home and directly into the bedroom," it added.
"The Duke of Sussex confirms and welcomes the formal excuse from Splash News and Picture Agency. "
Harry and Meghan's official residence is Frogmore Cottage in Windsor, near London.
In 2016, Kensington Palace released a rare statement on Harry's behalf and criticized the parties' media declaration o ch noted that "his girlfriend Meghan Markle has been the subject of a wave of assault and harassment".
In a statement sent to the UK Press Association's news agency, Splash says it has always been acknowledged that this situation is a misjudgment and we have taken steps to ensure that it will not be repeated. We apologize for the Duke and Duchess for the distress we have caused.
CNN has contacted Splash for comment.