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.
Lobby group Family First said it was de-registered because of its lobbying against the Marriage Equality bill.
The national director, Bob McCoskrie, said they were waiting on an appeal against that decision to go to the High Court.
He said after the ruling, they told their lawyers to ask for the case to be dropped, or to speed up the process.
"It's dragged on for a while now. It's been totally unneccessary, and this case has really set a good precedent," he said.
The Sensible Sentencing Trust also intends to reapply as a charity, after it was deregistered for being too political.
Trust spokesperson Ruth Money said their temporary solution was to split the organisation - one side a charity working with victims, and the other a trust lobbying for law change.
But she said they will now reapply as one charity, because that split did not work.
"We have to have two of everything," she said.
"Donees are confused as to who they are donating to."
The Department of Internal Affairs took over the Charities Commission's role in 2012.
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.