Masked protesters have begun a campaign against the Auckland headquarters of Scientology New Zealand, as part of a worldwide movement against the church.

The protest, called Operation Reconnect, was organised by a global group calling itself Anonymous, which began its internet-based "War on Scientology" in January. It aimed to bring together families it says have been torn apart by the church.

The latest protest on Saturday was the third of its kind, held across the road from the church's Panmure headquarters.

Scientology NZ spokesman Mike Ferris said the protesters were "nuts" and he had received threats via phone and email. He said police had been alerted to the protesters' plans and that the protests were full of "religious intolerance and hate speech".

Participants said it was a peaceful protest and was not an attack on a religion.

"All we are trying to do is to create awareness as many people don't know exactly what Scientology is and what it teaches," said one of the 20 protesters at the latest demonstration. "We don't want to harm anybody."

The protester declined to be named.

Auckland City police communications manager Noreen Hegarty said Anonymous had the right to protest as long as it was peaceful.

Anonymous began its campaign when the Church of Scientology tried to remove a film featuring Tom Cruise, intended for Scientology members, from the YouTube website. The video was viewed by millions of people worldwide.

The local branch of the church has bought a $10 million building to house its Auckland headquarters.

Mr Ferris said the new church building at 136 Grafton Rd, which was once occupied by Whitecliffe College of Arts and Design, was bought using donations from church members around the world.

The new building would house about 100 staff, he said, and include a symbolic office for Scientology founder L. Ron Hubbard.

"We are putting our roots [down], we are saying this is where we are going to be," Mr Ferris said.

He estimated there were 5000-6000 Scientologists in New Zealand, although 357 people called themselves Scientologists in the 2006 Census.