Forest and Bird is campaigning to keep mangrove management under the control of the Waikato Regional Council saying the plants provide a vital form of coastal protection.
The organisation's worried about a local bill which would allow Hauraki and Thames-Coromandel District Councils to remove the mangroves without resource consent.
Ecologist Dr Rebecca Stirnemann says it's a risky move to allow local government to bypass the Resource Management Act.
"If you're managing ecosystems you should be managing it from a big perspective and district councils managing it from a very small perspective don't necessarily have that expertise, with the ecological expertise in-house," Dr Stirnemann said.
"And they don't have necessarily the financial expertise either to manage those sorts of resources."
Some locals want to speed up the process of mangrove removal without having to go through resource management consent.
But Stirnemann said the draft bill lacks detail and considerations for both environmental and ecological impacts if mangroves were to be removed.
"You need to do it under the Resource Management Act. We have mechanisms to look at it if it's appropriate or not.
"But it's not appropriate for district councils to be going and doing it separate, outside all the laws and regulations which protect our environment."
If the bill goes through it may well mean more mangroves are removed but Professor Karin Bryan, a coastal processes scientist at Waikato University, said mangroves perform an important role in the ecosystem.
"You need to think of each mangrove tree as a bridge pylon and if you look at the Waikato bridge crossovers you can see these big eddies of turbulence behind each bridge pylon," Professor Bryan said.
"Imagine each one of those trees Is removing all that energy from turbulence as those waves and currents come in. So they [the mangroves] have massive ability to remove energy from things that are actually quite dangerous."
Stirnemann said the district councils have not considered the financial repercussions of removing mangroves for coastal communities in circumstances such as tsunami or storm surges which could wipe out houses and property which mangroves currently act as a barrier to.
Professor Bryan said while it's important communities make their own decisions about their environment, many people "don't have enough information to make reasonable decisions".
And Bryan said a blanket removal of the mangroves won't solve the problem - as its sediment and nutrient loading that's causing them to keep growing.
"They need to solve the catchment issue and then the mangroves will follow. You can remove them but the sediment's still coming right.
"So unless we get our riparian planting in, and our buffering in our streams, and change probably the way we do our forestry to small patch cuts like they have overseas - we won't reduce sediment loading to the point that the mangroves stop growing.
"So there's just going to be this constant problem and rather than the beautiful sandy beaches that we're hoping for, all we are going to get is a bunch of stumps with a bunch of mud around them."
Thames-Coromandel mayor Sandra Goudie said the bill would give more power to local communities.
"By doing a local bill to empower communities it means they can establish their own management plan if they want to," Goudie said.
"So this isn't about necessarily about taking out mangroves everywhere. This is only taking out mangroves where a community decides that they want to take some out."
Both the Hauraki and Thames-Coromandel district councils support the bill which will give them full control of the mangroves.
With just two days remaining for submissions to be made, mangrove advocates are hopeful that central government will consider the greater benefits to the environment that mangroves offer, instead of just seeing them as a weed to be removed.