These were executed in April 2011, with computers and thousands of documents being seized during the raid.
Henderson has long-challenged the validity of the search and last year began a claim against the Attorney-General, seeking declarations the warrants were unlawful.
Henderson, and companies linked to him, also sought thousands of dollars in damages and a declaration the raids breached the Bill of Rights Act.
They alleged that the application for the warrants contained wrong or misleading information and that, because of the validity of the warrants, the search and seizure was unreasonable.
Although the case was due to go to trial later this month, it was called off after both sides cut a deal.
As a result, Justice David Gendall has declared that the search warrants were unlawful and their execution was inconsistent with the New Zealand Bill of Rights Act.
All other parts of the claim have been withdrawn and the parties will pay their own court costs.
"It has taken four years, and being a few weeks away from a court hearing, to finally get them [the police] to acknowledge what was painfully clear from day one," Henderson told the Herald this afternoon.