The penguin was found last Monday by a dog-walker on Peka Peka beach, about 60km (37 miles) north of Wellington.
It had apparently swum off course some 3,000km from its home in Antarctica.
Experts were at first reluctant to intervene as the bird was apparently in good health. But when it grew lethargic it was transported to Wellington Zoo.
A businessman has offered to ship the penguin - dubbed Happy Feet - back to Antarctica in February, when he will lead an expedition there. But zoo officials have said it may be moved to the sub-Antarctic before then.
Bed of iceThe bird's plight has attracted worldwide attention, and hundreds of people gathered on Monday to watch a leading gastroenterologist from Wellington Hospital perform the endoscopy on the bird at the zoo.
An X-ray is scheduled for Wednesday to check on the bird's progress in clearing any remaining debrisA camera on a tube was guided through the penguin's swollen stomach and intestines, which were flushed to remove some of the sand and small pieces of driftwood it ate after coming ashore on the North Island. It apparently mistook them for snow, which penguins eat for hydration and to keep cool.
The procedure went well and it was hoped that any remaining debris would pass naturally, zoo spokesman Kate Baker said.
The bird will be given medication to increase gut motility, and an X-ray is scheduled for Wednesday to check progress.
"It's positive news, but he's definitely not out of the woods yet," Ms Baker told the New Zealand Press Association, adding that the penguin was likely to need more medical work over the next three months.
The bird is now eating fish slurry, and has been standing and appearing more active than when it arrived at the zoo on Friday.
To help it feel more at home, the penguin is being kept in a room chilled to about 8C (46F). There is a bed of ice for it to sleep on.
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