"It was pretty exciting," Dr Argilla said. "It was a great release." The entire crew were on deck to say goodbye.
Tangaroa continued with its research mission to the Campbell Islands to survey stocks of southern blue whiting, a type of cod.
Voyage leader Richard O'Driscoll said the special passenger had been a good traveller.
"He's been a well-behaved passenger, except when our team have helped to feed him and he's shown them who the boss is with a peck or two."
Happy Feet made headlines when he was discovered on Peka Peka Beach, north of Wellington, and spent two months recuperating at Wellington Zoo from four operations, after eating sand and sticks - mistaking them for snow and fish.
Dr Argilla said he was fit and healthy and had "just as much chance" of surviving as other juvenile emperor penguins, which tend to swim alone. He could spend up to a year in the Southern Ocean before returning to Antarctica to breed.
Sirtrack, which has 25 years of experience in wildlife tracking, designed and built the satellite transmitter and created a website so people can watch the penguin's travels to Antarctica. So far he has zig-zagged in an easterly direction.
The KiwiSat 202 tracking device was fitted to Happy Feet's feathers using glue and tape. It is designed to fall off when he moults in March or April.
Follow Happy Feet's travels on www.nzemperor.com