Forest & Bird is calling for councils around the country to be more "thorough" when doing drainage work after the death of dozens of eels in Hawke's Bay.
The Hawke's Bay Regional Council stopped work immediately after the eels died during work on a drain that forms part of the Heretaunga Plains Flood Control and Drainage Scheme.
Hawke's Bay Regional Council group manager asset management Chris Dolley said it stopped the work as soon as they were made aware of the eel deaths.
A Department of Conservation expert believed the eels were shortfin and not the protected longfin species native to New Zealand.
Freshwater advocate for Forest & Bird Annabeth Cohen said more needed to be done to protect fish in waterways whether they were indigenous or not.
"There doesn't seem to be any requirements before this kind of work begins, assessments should be done to determine what sort of fish are living or using these waterways.
"Fish can use waterways for all sorts of things, some like to lay low or hide during the day and come out at night. There just needs to be some sort of ecological assessment before this kind of work is set to begin.
"If there's a native species in the water then they could be re-located so no harm comes to them."
The council currently uses two methods for clearing drains with a slotted bucket.
The preferred method in rural areas was to place the material on the bank of the drain, which gives maximum opportunity for any eels to be seen and return to the water body, Dolley said.
The second method was to place the material directly in a truck, which was used if the drain was alongside a road or orchards where placing material to the side of the drain wasn't possible.
A council spokesperson said it had already had discussions on Tuesday about how to do things better.
One option involved looking into a catch and release option with local iwi while other conversations were ongoing.