The samples are used by researchers to determine information about the seals' lives like what they eat, their health and about how long they've been around New Zealand, according to the NIWA.
They included instructions for how to identify and safely collect leopard seal scat, which they said is "good as gold" for researchers.
Researchers analyse seal faeces to assess the health and diet of seals in New Zealand waters.
They are now on the search for owner of the USB.
The sample in question was then sent back to the lab for study, where it was frozen for more than year.
Volunteer Jodie Warren, who sifted through the scat and found the memory stick, expressed concern for the animal who ingested the USB.
On it, they found several photos and videos of of what appear to be fur seals or sea lions on Porpoise Bay, about 96 kilometres away from where the scat sample was found.
A leopard seal swims in this undated file image
During the defrosting process, Magnan discovered something large and hard concealed inside the poo. After leaving the stick to dry out for a few weeks, the team discovered the files which may help to find the owner.
Even more surprising was that the memory stick was in reasonably good condition, considering where it had come from, NIWA said.
"It is very worrying that these unbelievable Antarctic animals have plastic like this inside them", she said.
NIWA tweeted a video from the memory stick, which shows frolicking sea lions and the nose of a blue kayak.
The photos scientists found on it are the only clues of its owner, and the agency is offering to return it to that person for a price.
New Zealanders are also requested to report all sightings of the animals, document their location with videos and photographs, and call a dedicated leopard seal hotline.
"The more we can find out about these creatures, the more we can ensure they are looked after", the institute said.