Passengers on Real Journeys' overnight cruises have spotted up to 15 penguins at a time preening and feeding at dusk and early morning along the rocky coastline - double the numbers seen in recent years.
There are thought to be only 2500 to 3000 breeding pairs left along the Fiordland and Stewart Island coastlines.
Real Journeys nature guide on Milford Mariner Richard Heyward said 28 stoat traps had been placed at key breeding sites around the Milford Sound coastline at Anita Bay, the Moraine, Penguin Cove, Harrison Cove and the Penguin Tree.
"The traps were installed five years ago, but we are now emptying, re-baiting and setting them every month, he said."
"The stoats will eat the eggs and kill young chicks so this year it has been amazing to see a significant increase in penguin numbers on the rocks and swimming around in groups."
The Fiordland crested penguins arrive along the coastline and begin building nests in July before laying their eggs in August.
At the end of August, the young chicks hatch and are at their most vulnerable until about November, when they get their adult feathers and start to venture out further into the water.
By mid-December, the penguins usually head out to sea returning in January to moult.
