Happy Feet is in a critical condition following a second operation to clear sand from his system.
The penguin was first spied on Peka Peka Beach on Monday by resident Chris Wilton after swimming 4000 kilometres from Antarctica.
Though the penguin appeared lively, four days of eating sand and sticks caused his condition to deteriorate.
Yesterday he was lethargic, occasionally trying to spit sand. About midday, Te Papa and Conservation Department officials whisked him to the zoo in a chiller.
Vet science manager Lisa Argilla assessed the 27-kilogram bird as dehydrated, stressed, suffering from heat exhaustion and struggling to swallow - but still feisty enough to kick and struggle as she sedated him.
Penguins in the Antarctic eat ice when trying to cool down, and he was trying to do the same with sand, Te Papa terrestrial vertebrates curator Colin Miskelly said.
Last night he underwent a four-hour operation to clear his airway.
This morning he went under again as vets tried to clear his stomach of sand.
X-ray have shown there is still sand in the bird's stomach and he will need a third operation.
At the zoo's operating theatre last night, a captivated crowd of about 50 watched through the glass as vets worked quickly, discussing where best to insert a catheter and squeezing antibiotic ointment into his sand-filled, ulcer-covered eyes.
Gently, Argilla began to squirt water down his throat. Moments later, sand began cascading into a bucket.
His long-term future remains unclear, with DOC's Peter Simpson saying he will be in discussions with penguin experts and other parties.
"We have a dilemma. There is no transport to Antarctica this time of year ... we'll just have to take it day by day."
The last known emperor penguin to arrive on New Zealand shores was at Southland's Oreti Beach in 1967. It was released into Foveaux Strait.