The judge ruled on Thursday in London that Thames Valley Police had relied on the wrong legislation when seeking court approval for the warrants days before the raids in February. Mountbatten-Windsor applied for the warrants to be quashed, and the force conceded the error.
"We accept the position that the initial court's decision to issue warrants under the specific piece of legislation used was incorrect and therefore these must be legally quashed," a Thames Valley Police spokesperson said.
The decision casts doubt over the evidence gathered during the searches and over whether the former prince may ever be charged. He was arrested on suspicion of misconduct related to his ties to sex offender Jeffrey Epstein.
The ruling is the latest development since the arrest drew international attention, and it leaves police to determine whether any material seized during the searches can still be used in the investigation.