A set net ban to protect hoiho off the Otago Peninsula will be made permanent to reduce the risk of fishing bycatch.

A temporary emergency closure was imposed by the Oceans and Fisheries minister last year to protect the nationally endangered yellow-eyed penguin.

Shane Jones said he decided to make the closure permanent.

"I am also establishing a new escalating response framework called a fishing related mortality limit so I can act quickly and decisively to increase protections if needed," he said.

The plan included setting an accidental capture limit of four northern hoiho per year.

Jones called that a "bottom line" and did not rule out putting further restrictions on fishing in place to ensure the limit was not exceeded.

"Last year's risk assessment projected that to stabilise the northern hoiho population we must cut deaths from all causes by half and I consider the new protections will achieve this goal for fisheries bycatch," he said.

Disease, predation and starvation were the major risks to hoiho but the changes to reduce risk of fisheries bycatch would help, he said.

The changes would come into force on 16 September.

When Fisheries New Zealand was consulting on the changes last year, it said commercial set net fishing was estimated to be the third largest cause of hoiho mortality in recent years.

No hoiho were accidentally captured by commercial fishers in the January to March quarter this year.