Legislation that would allow the Government's electronic spy agency to legally gather information on New Zealanders passed its second reading in Parliament.

The Government had support for the Government Communications Security Bureau and Related Legislation Amendment Bill, including votes from independent MP Peter Dunne and ACT Party leader John Banks.

The bill passed by 61 votes to 59 on Thursday afternoon. It will be back before Parliament next Tuesday for committee stages.

Its passage through the House has prompted nationwide protests by people concerned about the power it will allow the Government Communications Security Bureau to wield.

One objection is that the GCSB is part of an international spy agency network, through which New Zealanders' private information will be shared. Another point of contention is that the bill will only just scrape through with a one-vote majority.

Attorney-General Chris Finlayson told Parliament that the public was being misled by ill-minded fear-mongering.

"This legislation is not a revolution in the way New Zealand conducts its intelligence operations and national security. It is not a case of expanding the borders of some intelligence empire."

Opposition parties say the legislation is dangerous and deeply flawed.

Labour leader David Shearer said the party accepts there are problems with the country's intelligence agencies, but the bill has been "a complete train wreck" and Prime Minister John Key has not justified the proposed laws.

"I asked John Key if he had any evidence that New Zealand would be more at risk if this legislation was not passed through. And he simply could not make that case."

Mr Shearer said Mr Key should be made to justify why the legislation is needed.

New Zealand First leader Winston Peters expressed his disgust at the Government's disregard for cross-party support for the bill.

"We'd like to be on the Parliamentary record that New Zealand First was prepared to seriously deal with this legislation, provided a number of safeguards were included. Sadly, this Government has not taken that approach, nor has it generally sought to work across the Parliamentary divide."

John Key was not in Parliament for the vote, but told reporters in Rotorua on Thursday that New Zealanders trained in camps overseas by al Qaeda are being monitored in the country but have not been arrested.

In 2011, it was revealed a man with alleged connections to al Qaeda was living in Hamilton, but Mr Key said at the time he did not pose a threat.

Outside the House, Green Party co-leader Russel Norman said on Thursday he wanted to know if that case is the one Mr Key is now using to justify the GCSB legislation.

"The Prime Minister bought up Mark Taylor before, told us he wasn't a threat. So is that the same person he's bringing up now and telling us is a threat? I don't know the answer to that - but I'd like the Prime Minister to answer."

Mark Taylor has denied the links.

Before the vote, Independent MP Peter Dunne said he would not reconsider his support despite revelations a reporter had her phone records released to a ministerial inquiry into the leaking of a report into the GCSB.

Mr Dunne has said the man leading the investigation, David Henry, went too far when he sought the records of Fairfax Media journalist Andrea Vance, but would still support the legislation.