The case dragged on for five years and resulted in the security risk certificate against Mr Zaoui being dropped.
Outside court, Dotcom said he understood the FBI had been able to view information gathered by the GCSB.
He said intercepted phone calls and information on his internet use could have been added to the US indictment which will be the subject of an extradition hearing in March.
"If they got it and if it was illegal that might indicate that parts of the indictment are also tainted by this.''
Earlier, his lawyer Paul Davison QC told the court that information from the Crown suggests there could have been more spying by the GCSB.
"Material from the FBI may well have been sourced by the GCSB and having been sent to the FBI may have come back,'' Mr Davison said.
The GCSB was spying on Dotcom unlawfully after being told by police that he and his associates were foreign nationals
Police gave the assurance all four were foreign nationals despite Dotcom and his Dutch co-accused Bram Van Der Kolk being permanent residents of New Zealand.
The GCSB is forbidden by law to spy on New Zealand citizens or permanent residents.
Chief High Court judge Justice Helen Winkelmann said she was "concerned'' the GCSB did not know Dotcom's residency status.
Mr Pike replied that there was an investigation underway.
The wrangle over the GCSB's involvement is the latest in a series of legal missteps by police and other agencies involved in the January 20 raid on Dotcom's Coatesville mansion.
The courts have also heard legal arguments over the use of search warrants later found to be invalid and the seizure of Dotcom's cash, cars and property using a court order which should never have been granted.
Information about the GCSB's involvement was kept secret last month as Acting Prime Minister Bill English had signed a "ministerial certificate'' which effectively suppressed it.
That certificate was released to APNZ today and shows Mr English directing the police not to disclose any information concerning the GCSB's involvement.
Mr English said doing so would "likely prejudice New Zealand in relation to the detection or prevention of serious crime by inhibiting the free and candid flow of information to and from the Bureau...''
Dotcom, van der Kolk, Finn Batato and Mathias Ortmann are accused of being behind the world's biggest criminal copyright violation through the file-sharing website Megaupload, which carried about 4 per cent of the world's internet traffic. The men deny the charges.