However, Talley's operations manager Andy Smith, of Nelson, said the dye was legal and non-toxic. The company had been using it since 2002 but it had been used in the US much longer.
It was also used by liferafts to increase visibility to searching aircraft and to colour American harbours green on St Patricks's Day. It dissipated within an hour.
"I'm pretty comfortable with it. We don't often fish inside the 12-mile limit anyway, and anything outside that has nothing to do with the Northland Regional Council."
The company had provided "plenty of information" to the council about its use of fluorescein, Mr Smith said.
The Northland Regional Council confirmed it had received a complaint about use of the dye.
Spokesman Murray Soljak said the council had written to the fishing company concerned asking it to demonstrate that the practice was legal. The council had also requested data on the substance being used.
Mr Morris said skipjack tuna were an important part of the food chain for dolphins, sharks and marlin. Any curbs on the use of fluorescein would help those species as well as preventing contamination of Northland waters.
Fishing companies used to use tuna bombs for the same purpose but found the dye was more effective, he added.
Fluorescein was first used to dye the Chicago River green on St Patrick's Day in 1962. However, it was replaced with a vegetable-based dye in 1966 at the urging of environmental groups.