Acting whip Senator Nick McKim announced the decision after the party met in Melbourne on Wednesday.
Some of Senator Rhiannon's colleagues have accused her of undermining a potential deal with the Turnbull government on schools funding by authorising leaflets in inner Sydney against the Gonski 2.0 policy.
She opposed the policy, in line with her state party, and insisted she has been faithful to Greens policy and process.
At Wednesday's meeting the party said it had highlighted a "structural issue" and requested the National Council work with Greens NSW to stop NSW MPs being bound to vote against a decision of the Australian Greens party room.
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A motion "that NSW Senators be excluded from Party Room discussions and decisions on contentious government legislation, including within their portfolio responsibilities, until these issues are resolved" was supported by
all MPs except Senator Rhiannon and Adam Bandt.
Earlier South Australian senator and Greens education spokeswoman Sarah Hanson-Young called for unity.
"People are upset," she told ABC radio.
"But overwhelmingly what I am hearing from our Green supporters here in this state is ... get on, sort this out, start working together.
"Because it is important that we have a strong Green voice in the parliament and we can only do that if we're not divided."
Senator Rhiannon has rejected media reports she had been "censured" by colleagues twice before.
But it is understood colleagues have criticised her in the past for breaching party discipline.
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Many grassroots members of the Greens have come out in support of Senator Rhiannon, while others back disciplinary action including possible expulsion.
Former leader Bob Brown has called for her to step down.
Greens leader Richard Di Natale has been championing a more pragmatic and "responsible" approach by the party, involving working closely with the coalition government.
But some elements of the party fear it will undermine the party's progressive base.
