Harry and Maghagen were forced to leave their homes after the photographs were published in the markets, including the Times, a royal source familiar with the incident told CNN.
"Splash News" launched a helicopter in January to take pictures of the couple's private home in the Cotswolds area of England, which Buckingham Palace said put the safety of the duo at risk.
"The syndication and publication of the photographs greatly undermined the safety and security of the duke and the house, to the extent that they are no longer able to live in the property," the palace said in a statement.
"The helicopter flies over the house at a low altitude, allowing Splash to shoot and the living area and dining area of the house, directly into the bedroom," he added.
"The Duke of Sussex acknowledges and welcomes the official apology from Splash.
The official quarters of Harry and Megan are the Frogum Cottage in Windsor, near London.
In 2016 Kensington Palace published a rare statement in Harry's name criticizing the couple's media coverage, noting that "his girlfriend Megan Marca is being exposed to a wave of abuse and harassment."
"He has always recognized that this situation represents a mistake of judgment and we have taken steps to ensure that he does not repeat himself," said Splash. "We apologize to the Duke and the Duchess for the distress we have caused."
CNN has contacted Splash for a comment.