Non-profit groups originally denied charity status for being too political plan to re-apply after the Supreme Court ruled political activity should not make a difference.
The ruling was a victory for Greenpeace, which fought through the courts for five years to regain the right to be considered a charity.
Organisations with charitable status do not pay income tax, can apply for different grants, and their donors are eligible for rebates.
Internal Affairs Minister Peter Dunne said this latest ruling turned the existing understanding of charity on its head.
“The argument has been that what people are supporting when they make a donation is the charitable work of those organisations, and that is normally pretty clear and tightly defined,” he said.
“To now say there is a political or other advocacy component to this is going to change the equation.”
Mr Dunne said it was too early to say what impact the ruling could have, but there may be a need to clear up the law further down the track.