X-rays have revealed that the young emperor penguin that travelled more than 3000km from its Antarctic home to a Kapiti Coast beach faces an uphill struggle to survive.

The penguin - nicknamed Happy Feet - was packed in a chilled box and taken from Peka Peka beach to Wellington Zoo, an hour south.

Veterinary staff put the penguin under a general anesthetic to take x-rays and pump sand from its stomach.

"We got a lot of it out, but there's still a large amount that's very likely left in its stomach. And that can cause a lot of complications, so we really need to get it out," said Wellington Zoo vet science manager Lisa Argilla.

"We'll probably have to knock him out again tomorrow, and stomach flush him again."

No twigs or branches had been found in the penguin's stomach yet, she said, "but he was apparently witnessed eating sticks, so it's very likely they are in there".

Ms Argilla said the penguin was badly dehydrated and had been put on an intravenous drip.

"Normally these guys eat snow, and that rehydrates them. That's why he's been eating sand, because he doesn't know any better."

Feathers would need to be DNA tested to determine its sex, but an Australian expert had estimated the penguin to be about 3 years old.

Ms Argilla said it was too early to estimate the penguin's chances of survival, but it would be "amazing" if it pulled through.

"They can tolerate a fair amount of punishment, but it is a lot of sand that he's got in his intestines at the moment."

She said if the penguin did regain strength the best option would be to release it as far south as possible.

Boats or planes do not journey to Antarctica during the winter.

The only other emperor penguin to arrive in New Zealand was released in Foveaux Strait in 1967.

Kelly Tarlton's Antarctic Encounter in Auckland would not offer a long-term solution as it houses only subantarctic king and gentoo penguins.

"There are some zoos in the US that have emperor penguins, so I guess we could explore that option if it reached a point where we can't release him in subantarctica," Ms Argilla said.

Department of Conservation programme manager Peter Simpson said the penguin's condition had worsened in New Zealand's warm climate.

"Just remember that in Antarctica it's currently 24 hours' darkness, and probably about 30C or 40C below zero."

Both Mr Simpson and Ms Argilla were stumped why the penguin swam about 3200km to end up on the Kapiti Coast.

"There's a possibility that he just got stuck in a current, or he might be unwell," Ms Argilla said. "Or he's just on a big overseas experience. And there is the World Cup coming up."