Renewals of more than 350 marine farm applications in the next eight years could cost millions of dollars, says the Marlborough District Council.
Mayor Alistair Sowman said future management of the aquaculture industry in the Sounds had been excluded from a new environment plan, because it was likely to be controversial.
He said the Marlborough Environment Plan had been 10 years in the making and would soon go out to the public, but it excluded matters around coastal management.
"The provisions that related to the use of the coastal environment had particular challenges yet to be resolved, and the council wanted to ensure that all care was taken - the processes and the solutions had to be robust," he said.
Mr Sowman said the farms were put in place before the Resource Management Act (RMA) and would need resource consent when renewals were sought in 2024.
"Before the RMA they operated under licences and the bar was low. If you look at a map we have a ribbon development right around the Sounds.
"Potentially all renewals have to be done individually and it's a huge task. It's going to costs millions of dollars and each renewal could be challenged so we need a better solution, and we need to identify better sites for aquaculture," Mr Sowman said.
Mr Sowman said the government had told the council it needed a better mechanism for looking at the future of aquaculture, as operators faced a costly process and the region sought a better solution for its environment.
"This gives us an opportunity to look at better planning for what might happen in 2024 when 350-plus marine farms come up for renewal. There's been a lot of talk with the industry, the Ministry for Primary Industries and residents, and we need more discussion on how we deal with site allocations ahead.
"Marlborough is an inland waterway that presents different challenges. It is a limited resource and we need to know how to manage it, but we now have better science that will help our decisions," Mr Sowman said.
He said the council needed to know where the best places for aquaculture might be and some marine farms might have to be moved.
The Marlborough Plan guided the use, development and protection of the region's natural and physical resources.
"As a council we are tasked with providing for aquaculture in appropriate locations but these have yet to be defined. We've pulled it out of plan because we don't want it holding up the whole plan, and we need a better mechanism to look at the future of aquaculture in the Sounds," Mr Sowman said.