A New Zealand government intelligence base is not "under US control or assisting military operations in Iraq", the country's spy chiefs say.

The rare public statement comes after three activists were cleared of burglary and wilful damage last month after breaking into the base in 2008.

The activists claimed that the intelligence centre in the country's South Island was under US control.

The Waihopai Valley base contributes to "torture" and "war", activists said.

"The Waihopai station was not - and is not - being used to contribute to 'torture, war and the use of weapons of mass destruction'," the director of the Government Communications Security Bureau (GCSB) Bruce Ferguson and his predecessor Bruce Tucker said in a statement.

"The claims that the Waihopai station is 'a United States spy base in our midst', contributing to ...'unspeakable evil' cannot be left unchallenged.

"It is totally operated and controlled by New Zealand, through the GCSB as an arm of the New Zealand government", they added.

Teacher Adrian Leason, Dominican friar Peter Murnane and farmer Sam Land deflated the Waihopai base's radar dome covers when they broke into the site in 2008, the news website stuff.co.nz reports.

The base undermines New Zealand government policy by helping military operations in Iraq, the activists claimed.

Reports in the New Zealand media say that the Waihopai listening post is part of the US-led Echelon eavesdropping network.

The Waipohai site, in the Marlborough region on the northern tip of South Island, is a regular target for activists who want to have the base closed down.