One party source said the effect of the rule change would be to wipe out any debate on grassroots-sponsored remits at the Greens' conferences.
The requirement that the backers of any remit would have to get the endorsement of a branch in another region would require driving hundreds of kilometres around the country to lobby other members.
"It wouldn't be worth the effort," one party member said.
Green Party Mt Eden branch convener Jeremy Hall said in the party newsletter Te Awa that there was irony to Greens' holding a conference on democracy because its rule changes would make it near-impossible for branches to raise issues and participate in the internal democracy of the party.
He added: "It will turn branches simply into volunteer units to just do fundraising, leafletting and campaigning, where their input into how the party is run will no longer be welcome."
The concerns came from a minority within the party - the remit was believed to have passed with around 80 per cent support.
Party co-convener Georgina Morrison said that there was some contention about the amendment, which the party felt was "normal and healthy".
She said the party was always working to be more professional and to have high-quality remits, but any important grassroots proposals would not be censored from the party's annual meeting.
If issues raised by the party's local branches were not dealt with at the annual meeting, they could be raised at other party meetings.
One Greens member was suspicious about the timing of the rule change, believing it had been done before next year's election to stifle any internal criticism of the Greens' performance in any subsequent coalition with Labour.
Ms Morrison dismissed this as "absolutely ridiculous", and said the Greens were already planning how their executive and MPs would continue to remain engaged with members as the party grew larger, or if it entered Government.
"We want to take the membership with us."
Remits debated at the annual meeting influenced how the party was run, but did not determine Greens' policy.