The judgment also recorded Dotcom's suspicions he had been spied on at least six weeks before the GCSB admitted to doing so, and sought details as to whether others had been swept up in the illegal operation.
The Crown had raised concerns about "secrecy", saying revealing the information could "compromise New Zealand's national security interests".
Justice Winkelmann said the concerns - which included revealing how the GCSB worked with "intelligence allies"- could be managed through the appointment of Stuart Grieve QC. Mr Grieve was appointed by the court to view top secret information and judge its relevance to the case.
The judgment also raised questions about evidence given by Detective Inspector Grant Wormald, the officer who commanded the raid on the mansion. It said evidence he had given about possible "live footage" of the raid "contradicted" earlier evidence given during the hearing.
The police were ordered to provide evidence from a senior New Zealand officer in the US who told an internal publication he "monitored" the raid from FBI headquarters.
Mr Wormald is also facing questions about other testimony after he assured the court there was no surveillance other than that carried out by police. The GCSB's illegal spying operation later emerged.