New national guidelines will apply to instream structures so fish can move freely around waterways.

The New Zealand Fish Passage Guidelines were launched yesterday, with recommendations for waterway managers, environmental officers, iwi and local communities in designing instream infrastructure to provide for fish passage.

The first guidelines of their kind, they were developed by Niwa, the Department of Conservation and the New Zealand Fish Passage Advisory Group to set the foundation for improved fish passage management in New Zealand.

Fish ladders, tiny doors and climbing ropes are among methods used by Northland environmental authorities to make local streams and canals more fish friendly.

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Even so, thousands of eels and other fish such as kokupu are impeded by structures or end up minced in the mangle of floodgate pumps and other mechanisms in those waterways.

"Many fish species, including some that used to be widespread, are now absent from many of the streams they used to occupy,'' Conservation Minister Eugenie Sage said at the document's launch.

High among threats to fish breeding and migration patterns are badly designed, sited and maintained obstacles like dams, weirs and culverts, and habitat loss from drainage, declining water quality, reduced flows and loss of spawning sites, Sage said.

Local fresh waterways and indigenous fish advocate Millan Ruka said while it was good to have a standard set down, the matters dealt with were already legislated for in the Resource Management Act (RMA).

DoC and authorities such as Northland Regional Council (NRC) have specific responsibilities to manage fish passage under the Freshwater Fisheries Regulations 1983 and the RMA.

Urgently needed was a local plan to rectify known hazards, he said. Also required for sustainability of freshwater fisheries was greater support and access for iwi and hapu to comprehensively monitor the number and health of tuna (eels) and kokupu, Ruka said.

An NRC spokeswoman was not available yesterday to say whether old structures that don't meet the now minimum design standard would now have to be rebuilt or modified.

Forest & Bird has welcomed the guidelines.

"Our native freshwater fish need to migrate up and down stream in order to feed and breed, especially those that spend part of their lives at sea," said freshwater advocate Annabeth Cohen.

New Zealand has 77 species of freshwater fish of which 57 per cent are indigenous, most of which are found nowhere else in the world.

A shocking 41 of those native freshwater species are threatened, at risk of extinction or even extinct; a higher proportion than almost any other country in the world.