Seals often came ashore to rest during rough weather and were naturally very good at social distancing, Dr Agnew said.
Fur seals were not a threat to little penguins, but their increased presence could make the birds nervous, she said.
However, the seals usually returned to sea in the afternoon, so penguins had no trouble entering the colony as usual each night, she said.
While the colony was closed for evening viewings or tours, a small number of staff continued to feed and care for sick or injured penguins in their care, under the essential service category, behind locked doors.
Earlier this month, there were nine birds at the colony's rehabilitation centre.
All but one yellow-eyed penguin had been released.
- Otago Daily Times