A motion to amend Section 28A of the act to allow these changes didn't carry, but the Northern Land Council is still concerned about the lack of consultation.
The Indigenous Affairs Minister Nigel Scullion introduced the changes and the debate was quite heated.
The minister had to be reminded to address the chair and not the Northern Land Council representatives sitting in the gallery.
In its submission, the Northern Land Council spelt out what it thought the potential dangers were.
Some of the changes could allow some functions to be transferred from land councils to local corporations, including the power to grant township leases and consent to mining exploration.
Northern Land COuncil chief executive Joe Morrison said he's more concerned about the lack of consultation around the issue.
"We want a better dialogue going forward."
Labor senator Nova Peris also represents the Northern Territory and she agrees.
"No real meaningful consultation was carried out, that's what black people are sick of," senator Peris said.
The Minister can't reintroduce changes to the bill for at least the next six months.