Many smaller parties have been squeezed in the last election, while some have been all but eliminated.
ACT Party leader David Seymor said it was nearly impossible for smaller parties to retain their distinctness when going into government.
He said ACT had survived, but has been highly damaged, while the Māori Party and United Future were driven out of Parliament.
"You have to vote for things with which you do not agree," he said.
"Your brand gets merged with another party."
Mr Seymour said the Green Party had demonstrated an awareness of the risks and tried to distinguish themselves, but faced "a very fundamental challenge" in maintaining their diversity.
Māori Party leader Marama Fox agreed that being in government with the National Party had been difficult.
She said Māori had wanted the party to go with Labour.
Her advice to the Greens was to make to take a stand against Labour and New Zealand First policies they did not agree with.
"If you disagree that mining and deep sea oil drilling should continue, stand up and say so," she said.
"If the Greens want to carve out a place for themselves, stand up and make your position clear."
Ms Fox said the Māori Party had variously been blamed for homelessness and poverty, despite voting against the government on those issues.
Green MP Julie Anne Genter said her party was aware of the risks of going into government and had prepared itself for it.
"I think we built up to a place where we thought it was very vitally important that we had certain ministerial roles, in order to achieve the policy gains we really wanted," she said.
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