"Some of them are still off-shore and some are in New Zealand.
"The fact someone might have a link might be the sort of reason the Government raises a warrant to observe their behaviour. It doesn't necessarily mean they've broken the law at this point."
Labour leader David Shearer said Mr Key was scaremongering, but refused to say whether he had also been briefed about al-Qaeda links.
"I can't really see his point. I think it's yet another one of those episodes when John Key is in a hole, he brings out the weapons of mass distraction."
Mr Key said much of the opposition to the bill was misinformed. "People can't have it both ways. They can't say potentially there is a risk which we need to monitor, and then say we don't want you monitoring anyone."
Attorney General Chis Finlayson made it clear in his speech to Parliament that the GCSB would require a warrant to collect metadata in the same way as any other data. Metadata is basic phone and internet logs, and some submitters had raised concerns that a grey area meant the GCSB had the power to harvest phone logs in bulk, as in Britain under the Prism programme.
Opposition MPs also attacked Peter Dunne for his support of the bill after initially opposing it.
Labour's Phil Goff said the Government was rushing it through despite warnings from the privacy and human rights commissioners.
"This Government is relying on two discredited MPs to pass legislation that we should be very cautious about."
Mr Finlayson said much of the criticism of the bill had been "misinformed". He said national security was vital for maintaining freedoms and keeping a country safe.
"But equally national security legislation must not have grey areas of uncertainty or doubtful interpretation that allow the state to gradually extend its activities and creep into ordinary people's private lives like some growing shadow."
The bill was written after the Kitteridge report found 88 cases in which the agency might have spied unlawfully on New Zealanders on behalf of agencies such as the police and SIS.