The number of fish being collected under customary permits is unknown, because records are incomplete or are not being provided by the kaitiaki, or guardians, who are supposed to ensure the fisheries remain sustainable.
The permits, for which the usual legal limits on numbers and sizes do not apply, have been available for tangata whenua since the late 1990s as a means of providing customary fishing rights under the Treaty of Waitangi (Fisheries Claims) Settlement Act 1992.
Fish taken with a permit are for customary use and cannot be sold.
When the government sets total allowable catch limits for fisheries, it makes provision for fish taken by all users, including customary ones.
Kaitiaki responsible for issuing the permits are required to provide quarterly reports on the number of permits issued, and total catches.
But information provided to The Dominion Post under the Official Information Act shows this is not always being done and the Ministry of Primary Industries does not know how many permits have been issued in the past three years, or how many fish have been caught.
It knows that at least 3446 permits were issued between January 2010 and November this year, but the total number could be much higher, as records are incomplete.
Hundreds of thousands of fish were caught, but some catches were recorded as "bins", "sacks" or "kgs" or details were not provided.
Ministry guidelines require the quantity to be recorded, as well as any minimum size stated by the kaitiaki.
The most harvested species was Foveaux Strait oysters, with 322,498 taken under customary permit last year and 258,418 in 2010. Other popular species were southern toheroa, with 39,659 taken last year, and crayfish, paua and kina, with tens of thousands taken around the country.
Permits are issued for designated special management areas, or rohe moana, of which there are more than 40, covering all of the South Island and 35 per cent of the North Island's coastline.
In other areas, kaitiaki can issue "Regulation 27a" permits for fish destined to be used in hui or tangi.
There are more than 430 kaitiaki covering the rohe moana of the North and South islands.
A ministry spokeswoman said "a key focus for future work is extending customary reporting coverage and improving data collection".
There was no penalty for failing to provide quarterly reports, but ministry staff contacted those who did not report, she said.
"As the requirement to report customary catch is not yet in place nationwide, customary data is insufficient in some fisheries to accurately determine customary catch.
"Where customary reporting is in place, data quality varies. In such cases the minister for primary industries uses the best available information to estimate customary catch when setting TACs."
- The Dominion Post