The Maori Party has already secured significant concessions in the reforms, including a requirement for iwi to be involved earlier in the consent process in sensitive cases.
It supported the legislation at the second reading on Tuesday.
But co-leader Marama Fox said its ongoing support hinged on National amending the clause that related to ministerial powers.
She suggested that the legislation could include a "carve-out", which allowed the minister to over-rule other activities but not GMOs.
Auckland Council, Hastings District Council and Northland Regional Council have introduced GE-free policies.
Federated Farmers is challenging the Northland and Hastings policies in court.
CANDIDATE IN A TOUGH SPOT
The RMA reforms put Hastings Mayor Lawrence Yule in a tricky position.
He is National's candidate in the safe seat of Tukituki and is likely to enter Parliament this year.
But he has also championed his region's GE-free policy, which the National-led Government's reforms will block.
Yule said he stood by his council's position, but accepted his own view could have to change if he became an MP.
"I do have a view that is different to the party," he said. "If I happen to get into Parliament I will talk to the caucus about it."
Hastings District Council introduced the ban so its food producers could brand themselves as GE-free on the international market.