Airline pilots are calling for an investigation into allegations of bullying and harassment after Auckland's rescue helicopter trust chief executive stood down.

The trust has today announced Greg Barrow's resignation saying it was time to allow new blood to assume the responsibility of taking the trust into a new era.

"He will take annual leave before formally departing on December 31," chairman Murray Bolton said today.

The New Zealand Air Line Pilots' Association welcomed the news - but general manager Dawn Handforth said she wanted to see an inquiry into both the trust's management and its governance board on the back of alleged bullying and harassment within the organisation.

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She said it had been an issue for a number of years and staff now felt the safety and wellbeing of themselves and the public were at risk.

"We need a full inquiry looking at all aspects of management and governance at the trust, to see how this was allowed to happen and to continue for so long," Handforth said.

"The staff are totally dedicated to their work and are only raising this now as they feel their safety and wellbeing is at risk.

"This must be addressed before an accident occurs."

She said individuals and businesses, who donated millions of dollars to the charitable trust, needed confidence the trust was "well run, well governed and the staff are fairly treated".