Thousands of Little Blue Penguins have been washing up dead on New Zealand's coast in recent months.

While the number of dead birds was unusual it was not unprecedented, Department of Conservation penguin expert Graeme Taylor told local news portal Stuff.

Penguin mass deaths are a one in 20-year event, with the last mass deaths being in 1998, he said.

The deaths were caused by changing weather patterns. During the penguin breeding season there was an El Nino pattern, with cold waters creating rich food supplies and leading to successful breeding.

But when La Nina took over in late spring the water warmed rapidly, pushing cooler currents to the bottom and with them the food supply.

"There is no estimate of the total numbers washed ashore but the rates that birds have been found on beaches suggest it is in the order of low thousands," Taylor said.

Many penguins also die after attempting to come ashore to moult at this time of year. If they don't have enough fat reserves they may not survive the two or three week process.

"They are coming out of it very, very weak and starving and then a combination of cyclones, offshore storms and bad weather has meant that they just don't have the energy to find food and fight the rough oceans anymore," Western Bay Wildlife Trust's Julia Graham told Radio New Zealand.

"By the time they're washing up, they're pretty far gone, they're emaciated, starving, no food, very, very exhausted."

Little Penguins are the world's smallest penguin species. They live around all of New Zealand's coastal areas and also around South Australia and Tasmania.