After the six-hour swim the birds needed to be checked over to make sure their feathers were completely waterproof.
Only six of the birds failed the waterproofing test and will be held back to get stronger before being released at a later date.
The penguins, released on Mount Maunganui beach at Shark Alley, between Leisure Island and Rabbit Island, were all brought in from areas nearby and Dr Gartrell said they should easily find their way home.
"We know exactly where each bird has come from. They're from Leisure Island, Rabbit Island and Pilot Bay. It's all within easy swimming distance for a penguin. They have a better navigational sense than we do. Most of the time they'll go back to the same burrows over and over again," he said.
No penguins were being released from colonies on Matakana or Motiti Islands or from the seaward side of Mauao because those areas were not yet considered clean enough.
Dr Gartrell said the salinity levels of the pools were being increased to get the penguins used to salt water again after spending so much time in fresh water pools.
Two shags were released on Sunday and Dr Gartrell said it was an emotional moment seeing the first birds released.
"I believe there were people with tears in their eyes. It was a brilliant moment. For a long time we've been in a holding pattern, it was starting to feel like it was going to go on forever. But it was great."
He said the first penguins would be another milestone but there was still more work to do at the centre.
"I tell you, it'll feel great [releasing the first penguins], but it won't feel as good as releasing the very last penguins," he said.
He said the centre expected to release birds in batches about every five days, depending on the penguins' preparedness. Of the 360 penguins taken into care, only about 20 have died.
Meanwhile, salvors battled winds reaching more than 40 knots (74km/h) to remove a further 21 containers from the stern of Rena. Seventy containers have now been removed.
Maritime New Zealand salvage unit manager Arthur Jobard said the salvage team had done well to remove so many containers in the windy conditions.
"They have still managed to remove a good number of containers, which is excellent."
Mr Jobard said containers landing ashore at the Port of Tauranga were being efficiently processed by container recovery company Braemar Howells.
"Two of the refrigerated containers that held the remains of rotting food came ashore today and Braemar Howells was able to process these within two hours.
"That's excellent progress - the contents of the refrigerated containers are quite nasty and it's good to see them move these through the process quickly."
National on scene commander Alex van Wijngaarden said warm water washing was done on Mauao yesterday to remove residual oil from the rocks. "Following the good results we have seen from this, we will be doing more of this work over the next few days."