The company says it is rare to see one and a permit would only cover incidental sightings, but a marine mammal scientist says an encounter is increasingly likely, and the impact tourism has on the mammals is undeniable.
The Department of Conservation has called for submissions on Real Journeys Ltd’s (trading as RealNZ) application to renew its permit with a "major amendment".
The amendment is to "view" marine mammals by boat in Fiordland, Southland (Murihiku) and Stewart Island.
It would allow RealNZ boats already out on tours that "happen to stumble upon a whale" to stop and watch them for 15 minutes.
It would apply to sightings of humpbacks, southern right whales and orcas.
Boats are not allowed closer than 50m to a whale and 200m to a female with a calf under marine mammal protection regulation.
RealNZ chief tourism officer Hannah Ballantyne said during migration periods, there was a chance some of their tours might encounter whales as they travelled between the east coast of Australia and Antarctica.
"This permit means that on the rare occasion these encounters happen, our guests can have a once-in-a-lifetime experience to view these beautiful animals."
Dr Rochelle Constantine said the population of humpback whales migrating up the east coast of Australia was estimated at around 40,000.
When they travelled to or from Antarctica, an unknown number, but at least a portion, come through New Zealand waters.
Since whaling stopped, she said the whales of East Australia had fully recovered, in abundance.
"The chance of seeing those whales is higher than it's ever been in the Fiordland area."
She said the impact tourism had on the whales was well documented and researched.
"You can't offset impact on the animal," she said.
"No new research is needed. It doesn't help the whales. We have the answers."
The whales were most likely to be seen in the southwest in September and October.
They came into the fiords and had been reported in Doubtful Sound and "a lot" in Dusky Sound, she said.
"They're curious whales. They pop into all kinds of places."
It was the time, also, when the whales were at their most vulnerable, as they had not been feeding for about six months during the migration period and many females would have their newborn calves with them, so "we have to be really mindful of not adding stress to them", Ms Constantine said.
She expected Doc would take everything into careful consideration.
"As they do for all of the Fiordland marine mammal tourism and tourism in general in Fiordland because it is such an important place," she said.
