The Antarctic explorer will now be held by Te Papa for future research.
The 2m-long female was spotted in Karitane on July 2 and Birdlings Flat, Canterbury, on July 7.
After weeks off the radar it was discovered on Saturday in the Hutt River, but died a few days later, as the Department of Conservation attempted to transport the emaciated animal back to the Wellington south coast.
Te Papa vertebrates curator Colin Miskelly said a necropsy would be performed on the seal so the museum could glean some more information about it.
Its hide and some tissue would be preserved, but researchers were particularly interested in its skeleton, he said.
Having intact skeletons of different seals created a useful reference point when researching older fossils.
Between 1885 and 2015 eight crabeater seals were found on New Zealand shores.
However, three have been discovered in the past three years, all of which are held by Te Papa.
''It's quite bizarre to have so many, but three means we can look at range of variability,'' Mr Miskelly said.
The increase in sightings could be because of better cellphone camera technology and citizen science websites, he said.
The animals live on pack ice in the Antarctic, where they are ''one of the most abundant large mammals on the planet''.
''They just live in a place where no-one gets to.''
It was likely the unusual cases which ventured north did so because there was ''something wrong with their compass''.
''I actually had a suggestion from a colleague that there are parasites that give animals weird behaviour. It might be something pathological.''
This could possibly be assessed during the necropsy.
When the animal arrived at Karitane it had injuries on its lower back which were thought to have been caused by a leopard seal or orca.
However, on closer inspection they were seen to be ''fairly long and linear'' and more indicative of boat propeller scars.
This was unlikely to have caused its death as the animals were ''quite resilient''.
''My hunch is once they come north they can't find the right type of food and become emaciated and weak.''