The tagged whale's route around the South Island - starting off Westport, going through Cook Strait and then down the east coast.

Scientists have tagged blue whales off the New Zealand coast for the first time this summer, with one of the animals heading north while the other went for a swim around the South Island.

The plan was to tag pygmy blue whales - which, despite the name, are not small - in the South Taranaki Bight in late January and early February, but storms and warm water made the job more difficult than expected.

Researchers from the Department of Conservation, the National Institute of Water and Atmospheric Research, and Blue Planet Marine tagged two of the animals off the coast from Westport last month.

DR KRISTA HUPMAN Researchers looking for blue whales were able to tag two off Westport in February.

"They are really difficult animals to tag. It's the hardest by far I have ever done. It's really tricky, Niwa megafauna expert Dr Kim Goetz said.

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"Generally when you tag these animals you want to find them while they're feeding at the surface... They're very pre-occupied."

DR KRISTA HUPMAN Altogether, about 15 blue whales were seen during the trip.

But because the water was so warm this summer, the blue whales that were found were feeding well below the surface, and only spending a few minutes on the surface between dives.

"These are big animals. They move quickly. You only have the first time to get close to them," Goetz said.

Whales that were travelling rather than feeding could be doing 35kmh. "You can't approach them."

To put a tag on, a team would work from a six-metre boat launched from the main research vessel.

"When you find a whale .. you need to be in a very fast little boat that can get close to them," Goetz said. A line thrower, used to throw lines between boats, was modified to get the tag onto the whale.

"There's a specially designed bowsprit built onto the little boat that basically has a platform on the front of the bow, where the tagger stands, and is basically strapped into that. You're kind of above and ahead of the whale to get the tag on."

The two whales tagged were probably 20 metres long. "It's very humbling when you're around these animals. They could really destroy your boat if they wanted to," Goetz said.

"You see these animals next to the boat and they are way larger, but they generally don't care," she said.

"The person driving the little boat is very experienced... To drive around these animals you have to understand the animal's behaviour."

One of the animals tagged headed north up the west coast of the North Island, until transmissions stopped when it was near Auckland. It was not uncommon for transmission to stop for a while and Goetz was hopeful signals would restart from that animal.

The other whale appeared to have been feeding in the Westport area before going through Cook Strait.

"It just went right through the strait and down the other side... It spent quite a bit of time in the Kaikōura area," Goetz said.

"Then it spent a chunk of time just south of Banks Peninsula, then it just kept heading south. It spent a little bit of time just off Stewart Island, then it came back north around the other side."

On the way up the West Coast it spent sometime around the Gilbert Seamount - about 550km west of Milford Sound.

"You can kind of make an assumption that the longer an animal is spending in an area, it's because it's found something to feed on," Goetz said.

Researchers needed a larger sample size, and it was hoped to develop a programme to tag more whales.

Pygmy blue whales tagged in Australia had travelled to New Caledonia then gone back south. It had been thought the two tagged off Westport might do something similar, perhaps head to Fiji. "We don't know anything about where their breeding grounds are."

It was thought the tagged whale that headed north might have been doing that "but we don't really know".

"We don't know what this one (the whale that swum around the South Island) is doing. I'm thinking this one is going to head north," Goetz said.

"So far it's done nothing we thought it was going to do."

It's thought the two whales tagged were pygmy blue whales, although that has to be confirmed from biopsies taken from the animals. Antarctic blue whales were also believed to come into New Zealand waters. The analysis will also show the sex of the two tagged whales.

Storms and much warmer than usual sea temperatures meant the researchers lost some of the days they had hoped to be at sea, and then didn't find any whales where they would normally have been.

Because the water was so warm it basically shut down the upwelling system, through which cooler water comes to the surface, driven by currents, winds and weather events.

As cooler water came to the surface it created a productive area where there was more phytoplankton in the water. That meant more krill, which blue whales fed on, Goetz said.

Usually there was upwelling in the area off Farewell Spit but not this summer, so when the researchers did manage to get into the waters off Taranaki they didn't find any blue whales.

By looking at satellite imagery and talking to tuna fishers, because tuna also eat krill, they ended up looking for blue whales further south. The two adult animals that were tagged were about 55km west of Westport in water that was about 200 metres deep, Goetz said.

"We only had a few days left. We thought at first we weren't going to get any tags out but we did get two."