The bird is nicknamed Happy Feet from a 2006 animated movie.
Doctors at the Wellington Zoo guided a camera on a tube through the penguin's swollen intestines and flushed its stomach to remove sand, sticks and stones from its stomach on Monday.
There's still more debris inside, but doctors are hoping hope Happy Feet will be able to pass the rest naturally.
Full recovery for the young emperor penguin - affectionately dubbed Happy Feet - may take months, and officials are unsure when or how it could return home to the Antarctic, about 2,000 miles (3,200 kilometers) away.
What's next for Happy Feet still remains to be decided.
The Associated Press contributed to this report.