The annual migration of the little understood pygmy blue whale has been tracked by scientists for the first time.

Scientists are only just beginning to learn about the animal, which was first described in the early 1960s.

The migration study has shed light on their habits and the risks faced during their 3,000 kilometre journey from Western Australia to Indonesia.

The pygmy blue whale is a sub-species of the Antarctic blue whale.

Despite its name, the animal is still enormous; about three quarters the size of the blue whale.

Scientists, including researchers from the Hobart-based Australian Antarctic Division, have successfully tagged 11 of the whales.

"It's the biggest pygmy you'll ever hear about," said AAD chief scientist Nick Gales.

"These animals get up to about 24 odd metres.

"They don't go as far south right down to the ice as the Antarctic blue whale, they live in the slightly warmer waters."

Total numbers are still unclear; there are somewhere between 500 and 1200 off Western Australia.

"We don't know what's out there, and we don't know where they're travelling, so we don't know what possible impact we might have on them," he said.

Tagging whales a challenge

Pygmy blue whale facts: Subspecies of blue whales

Subspecies of blue whales Grow up to 24 metres

Grow up to 24 metres Not blue - they are covered in pale grey and white mottles

Not blue - they are covered in pale grey and white mottles Distinguished by a tiny dorsal fin towards tail

Distinguished by a tiny dorsal fin towards tail Never been found beyond 50 degrees south

Never been found beyond 50 degrees south Feeding zones off WA and Victoria

Feeding zones off WA and Victoria Migrate annually to Indonesia

Satellite tagging will help paint a clearer picture, but attaching the devices is a challenge.

"We have to approach the whale really up close in a small boat and then we shoot a small tag onto its back."

"It's like firing a splinter onto the back of an animal. We fire a tag on and it just sticks in through the skin and into the blubber."

The tag transmits data to a satellite.

Scientists successfully tagged 11 of the whales in 2011 and the results have been published today in an international science journal.

The whales swam at speeds of about 20 kilometres per hour during the 3,000 kilometres journey.

The data has provided important information for whale researchers.

"We know that they go through areas where there's a lot of oil and gas activity and the industry are aware of these whales," Dr Gales said.

"They now know a bit more about when they might come through so they can take more action against impacting them.

The information will be shared with Indonesian authorities.

"We can inform the Indonesian government and scientists up there about what we have learnt about those whales and in the management of fisheries and vessel traffic around all of those areas."