After four days of travelling on the Tangaroa, the 26.6kg bird will be released into the ocean at a point east of Campbell Island.
The drop-off location is within the natural range of young emperor penguins.
Niwa was looking at two ways of getting Happy Feet off the ship, said the institute's general manager research Rob Murdoch.
"It depends on the sea conditions. One of the options is to have a slide at the stern of the ship so he can, under his own steam and time, slide down into the water."
The second option was to lower the penguin into the ocean in a workboat, from which a staff member would help get him back into the water.
Happy Feet will be travelling in style while on the boat. A Wellington Zoo team was developing a refrigerated crate that would keep the penguin cold enough, comfortable and safe during turbulent weather said zoo spokeswoman Kate Baker.
He has been living in a zoo enclosure kept refrigerated at temperatures between 0.5 and 2C.
He will be accompanied by Wellington Zoo veterinary manager Dr Lisa Argilla and two Niwa staff.
The Tangaroa was going to Campbell Island to make a month-long fisheries survey on southern blue whiting, so it was a good match-up of resources Ms Baker said.
Happy Feet has been preparing for his release by taking a few dips into a chilled saltwater pool next to his enclosure, said Ms Baker.
She said she expected Happy Feet to make the journey safely.
"Emperor penguins are used to going long periods of time without exercising."
Fans of Happy Feet can track his progress in the wild.
The penguin will be carrying a GPS tracker so his progress can be followed on the Sirtrack website and the Our Far South website.
Said Ms Baker: "It's been really amazing having him here, but it's going to be really good when he goes because it means we've done our job."
