The 2011 survey used a dog to sniff out ducks, which this year's did not, and a dog may have found more whio, Ms Jonas said.
The FLR Trust's work with whio at Maungataniwha is funded by Genesis Energy as part of the Whio Forever project - a five year $2.5 million dollar programme, managed by DOC, which will double the number of secure breeding sites around the country.
The Maungataniwha was classified under the project as a recovery site, which means it receives some form of pest control. Higher-priority breeding areas are classified as security sites.
The area has double the density of whio of other recovery sites, and similar results have been duplicated in informal counts elsewhere in the forest.
This indicates substantial populations are likely to exist across the southern Whirinaki and Te Urewera ranges, said Maungataniwha estate manager Pete Shaw.
"We're hoping these results indicate at least a partial plateau in the decline of whio across inland Hawke's Bay," he said.
"To get similar numbers from two surveys, conducted three years apart, is immensely encouraging."
The survey consisted of walking in or alongside rivers and streams, crisscrossing them and, in some cases rafting or tubing them, to look and listen for The Forest Lifeforce Restoration Trust was established in 2006 to provide direction and funding for the restoration of threatened species of fauna and flora in native forests within the Central North Island.