Centre manager Hoani Langsbury confirmed a chick was attacked and killed some time last week by what was most likely a stoat.
He said the culprit would have climbed the fence, at the breeding colony on the Otago Peninsula, something staff had seen before.
While the death was upsetting he said his team worked hard year round to keep predators out.
"We do predator control 365 days of the year and this would be an exception rather than something normal."
The Royal Albatross Centre relies heavily on traps and other predator management techniques to keep mustelid creatures like stoats away from the birds.
Those measures were heightened in February during breeding season for the pesky pests.
"The offspring are always moving away from where they are born which means they are always moving across the peninsula," Mr Langsbury said.
"People have said in the last six months that they have seen more stoats and ferrets, which means we have been doing more predator control."
The centre works in conjunction with the Department of Conservation to protect the birds.
Mr Langsbury said while his organisation and Doc would kill around 15 mustelids a year, stoats were strong swimmers.
"They can swim across the harbour. It’s a short distance they can make from Aramoana over to where we are."
However he was confident the end of the Otago Peninsula did not have a resident population of stoats, due to the extensive trapping done on the peninsula’s northern tip.
There are 24 chicks at the centre at present.