Thousands of people who took to the streets in 11 centres around New Zealand to protest against new spy agency powers are either politically aligned or misinformed, Prime Minister John Key says.

A march down Auckland's Queen Street on Saturday attracted an estimated 2000 people, while in Wellington more than 500 people walked to parliament to protest against the spy bill.

The bill will make it legal for the foreign-focused Government Communications Security Bureau (GCSB)to spy on New Zealanders on behalf of the Security Intelligence Service (SIS), police and Defence Force.

"At the risk of encouraging them to have more protests, I would have actually said those numbers were quite light - it wasn't anything like what we saw for mining or anything else," he told TVNZ's Q&A programme on Sunday.

"Secondly, a lot of people that would go along would be either A, politically aligned, or B, with the greatest of respect, misinformed."

Independent MP Peter Dunne has agreed to support the bill in exchange for changes, giving the government the one-vote majority it needs to pass.

Several protesters said they were concerned about the law change - although most admitted they had not read the bill.

Protester Claire Bleakley said New Zealanders should not be under threat of state-sanctioned spying.

"I'm really angry with the government for interfering in our private lives, taking away our security, and the fact that the information that may seem trivial to them but is very important to us is going to be, possibly, used against us," she said.

The GCSB has carried out similar surveillance in the past, believing it was legal, until last August when the Kim Dotcom court case raised questions about its legality - prompting Mr Key to change the law.

Mr Key says he will have to accept that he has not been able to drum up more parliamentary support for the bill.

"My options are either, pass it by one, or not pass it at all," he said.