Among them were native eels, which are born in the sea near Tonga, before currents carry them back to New Zealand, where they enter river mouths as glass eels.
"They need to be able to move upstream and find somewhere to live," Conservation Minister Eugenie Sage said today.
"Eels and many of our whitebait species, which also spend part of their life at sea, are struggling.
"We can help them thrive by ensuring that instream structures don't obstruct fish passage."
DoC defined migration barriers as "any structure that restricts the upstream and/or downstream movement of freshwater fish".
Currently, culverts and fords were not allowed to block fish unless they had been approved or exempted by DoC.
The requirement applied to newly-built structures, where approval should be sought before they were constructed, and to existing structures that did not already have an approval or which could no longer meet the requirements of the approval.
Dams and diversion structures in any natural river, steam or water built since January 1984 may also require facilities to let fish pass.
That excepted nets or traps used solely for taking or holding fish; dams constructed on dry or swampy land and used for watering stock or as habitats for watering birds; or water diversions not being incorporated into dams and which emptied into any viable fish habitats without dead ends.
The other exemptions were dam or diversion structures already subject to a water right issued under the provisions of the Water and Soil Conservation Act - or any structure authorised by a Regional Water Board not requiring a water right "that in no way impedes the passage of fish".
Forest and Bird freshwater advocate Annabeth Cohen called on regional councils to adopt the new guidelines so any new structure built will ensure safe fish passage.
"For example, when a regional council grants consent for a road over a stream, they are required to ensure safe fish passage, but our understanding is this doesn't always happen," she said.
"We also support the recommendation that, where existing structures are blocking fish movement, the first solution should be removal, with retrofitting a second option if removal is not possible.
"Councils need to prioritise fish passage, and these new guidelines are a great resource to help them."
The new guidelines follow revelations this year that masses of native eels have been killed while attempting to swim through pumping stations operated by councils.
New Zealand has 77 species of freshwater fish, 57 of which are indigenous and most of these were endemic so are found nowhere else in the world.
Nearly three quarters of them were threatened with or at risk of extinction or even extinct - a higher proportion than almost any other country in the world.
"Many fish species, including some that used to be widespread, are now absent from many of the streams they used to occupy," Sage said.
Local extinction was often the result of several threats operating together, she said, and native fish have had to contend with habitat loss from wetland drainage, declining water quality, reduced river and stream flows from water abstraction or diversion, loss of spawning sites and barriers to migration.
"Badly designed, sited, constructed and maintained obstacles like dams, weirs and culverts which block fish and eel movement up and down waterways and between rivers and the sea is a major threat to freshwater fish."
The guidelines are being developed by a new advisory group and further summaries were due to be released this year.
