The former Duke of York instructed lawyers after discovering detectives from Thames Valley Police had allegedly removed private and confidential material unconnected to the criminal investigation.
He launched a judicial review of the search warrants that granted police permission to raid his home in Norfolk and former residence in Windsor in February.
As well as challenging police over their conduct, his lawyers are asking the High Court to rule whether the granting of the warrant itself by an Old Bailey judge was lawful.
A ruling in the legal case is expected imminently, and if Mountbatten-Windsor wins, Thames Valley Police could be forced to return all the material seized in the raids.
Such a move would deal a potentially fatal blow to the misconduct in public office investigation that was launched following the publication of the Epstein Files earlier this year.
Mountbatten-Windsor, who remains eighth in line to the throne, was arrested on the morning of his 66th birthday, after being accused of passing market-sensitive information to his friend, the convicted paedophile Jeffrey Epstein, when he was United Kingdom trade envoy between 2001 and 2011.
The way police execute search warrants in high-profile investigations became the subject of intense scrutiny during Scotland Yard’s disastrous Operation Midland investigation.
Detectives investigating a non-existent VIP child abuse ring raided the homes of senior public figures, including Lord Brittan, the former home secretary, who had died just weeks earlier.
In a scathing review of the Met Police’s conduct, Sir Richard Henriques, a retired High Court judge, said officers searching Lady Brittan’s North Yorkshire home “acted as if they were looking for bodies or body parts”.
He also criticised the way detectives examined every piece of paper in the property, including letters of condolence and golden wedding cards.
The Met Police later paid out large sums in damages to those whose homes had been raided.
Jonathan Caplan KC, who represented Lady Brittan in the aftermath of the case, suggested Thames Valley Police may have gone too far.
He told the Telegraph: “A prominent individual’s reputation can incur substantial damage over a substantial period of time because of an erroneous decision at the outset of the investigative process. Operation Midland was an example of that.
“I expect that in the coming days we might hear that Thames Valley Police has to return exhibits and other personal belongings that they have taken from Mr Mountbatten Windsor as a result of these warrants but it will be for the High Court to decide if Thames Valley Police has acted unlawfully.
“You would have expected them to be ultra cautious in this case, so the fact that there is a legal challenge at all is surprising.”
Detectives spent several days searching properties linked to the former duke and removed a large amount of material.
He was questioned for about 12 hours at Aylsham police station in Norfolk before being released under investigation, but has not been interviewed again since.
Mountbatten-Windsor was granted permission for the judicial review earlier this year, but Thames Valley Police applied to keep the details of the legal claim secret.
A hearing scheduled at the High Court on Thursday will hear the force’s application to restrict access to court documents.
The hearing, before Justice Hilliard, will begin in private.
However, if the judge is minded to restrict access to the papers, media representations will be heard before a final decision is made.
The legal bill for the judicial review is expected to run into hundreds of thousands of pounds, but Buckingham Palace has made it clear that money he receives from the King must not be used.
Mountbatten-Windsor receives an annual six-figure stipend from His Majesty via his private funds, which includes an allowance made for the cost of private security.
A Buckingham Palace source said the monarch had no involvement in the judicial review application.
They added that it had been “made clear” to the former prince that the financial provision he receives from his elder brother should not be used to fund the High Court claim.
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