Fisheries Minister Stuart Nash says commercial and recreational catch limits for longfin eels could be cut to prevent numbers dropping further.
Mr Nash has asked his staff to investigate, after a survey funded by conservation charity Reconnecting Northland found no longfin eels large enough to breed in 12km of the Wairua and Northern Wairoa rivers.
"If people are saying 'look, 20 years ago we used to catch a whole lot of these, now we're not seeing anything, in fact the only eels we're seeing are less than one metre long', we need to take that sort of evidence seriously," Mr Nash said.
"If we need to takes measures in terms of cutting commercial and recreational catch, then we will do that."
Mr Nash said according to Fisheries New Zealand data, the commercial and recreational catch of the declining species was sustainable.
But he was asking his staff to sit down with the Northland survey-takers to discuss their findings.
Mr Nash said it was unlikely longfin eels would be removed from the quota system, because it provided the means to protect them if necessary.
The eel survey this summer was carried out by river campaigner Millan Ruka and Whatitiri hapu members.
Mr Ruka has called for rāhui, or temporary ban, on commercial longfin eel fishing to allow eel numbers to recover.
He said officials needed to rethink the way they estimated populations of the declining eel species.
The Ministry of Fisheries calculated eel numbers over an area from south of Auckland to Cape Reinga, but within that region, certain catchments were being hammered by commercial fishers, he said.
"Fresh water fisheries management definitely needs an overhaul," Mr Ruka said.
"Sections of our river are fished to the bone, there's nothing there.
"It's very good news that Minister Nash will look into it."
Some marae could not exercise their cultural rights to take eels, because there were no longer enough of the fish in the river, Mr Ruka said.
Although the longfin eel is classed as 'at-risk and declining', commercial fishers are allowed to take 34 tonnes of longfin eels a year from northern rivers.
The total allowable catch was reduced from 39 tonnes last year, based on estimates of the relative abundance of the fish.