The vessel dropped Happy Feet off 79km north of Campbell Island, roughly 621km south of New Zealand.
Happy Feet had been happily munching on hoki and has had fresh ice put in his crate since the ship set sail from Wellington on Monday.
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.''
He was due to be release on Friday or Saturday, but 40-50 knot winds and 6-8m swells kept the penguin on board the ship.
Happy Feet made headlines when he was discovered on Peka Peka beach on the Kapiti Coast in June. He was taken to the Wellington Zoo where he underwent four operations to remove stones, sand, and other matter from his stomach.
Now back in the water, Happy Feet can be tracked on the Sirtrack and the Our Far South website as he has been fitted with a Sirtrack satellite tracker and a microchip.