The team from Willowbank Wildlife Reserve was looking for the elusive South Island kōkako when they chanced upon the cave in Chalky Inlet last month.
The cave had a drawing of a galleon vessel and what is believed to be the names of its mariners etched underneath.
The remains of an old cannon were discovered nearby.
"You can’t help but wonder the history behind those names, why those men were there and what happened to them,” Willowbank managing director Michael Willis said.
The exciting discovery hinted of an unknown shipwreck, perhaps dating back to the age of exploration when Dutch, French, English, Spanish and Russian ships sailed New Zealand waters.
"If it had been in the later stages of exploration, people would have been more likely to know about it.
"The fact that people don’t know about it would suggest it is in the early days,” Willis said.
Willis and fellow expedition members Mark Willis and Dale Hedgcock unearthed the cannon late last month.
They were at a Chalky Inlet beach when they spotted a small, deep orange patch among the stones.
They moved the surrounding rocks with their bare hands.
"It was sheer luck that they saw it, it was a patch of rust and they knew that there was something underneath,” Willis said.
The discovery followed Willis exploring a cave he happened to see the previous month while walking along the same beach, and finding the scrawlings of names underneath the drawing of an old ship.
The cave and the cannon are only about 100 metres apart, pointing to the possibility the cannon is from the ship that is drawn on its wall.
The drawing of the ship is not detailed enough, however, to see if it has cannons or not.
Willis said there are at least four names. They are hard to read, but one appears to say “Jamie Rasmussen.”
Rock underneath had fallen off, and it appeared that originally there may have been more names.
Willis said the mariners could have perished in the area of the beach. It was also possible they were seen by local Māori or sealers. However, these potential rescuers would not be in the area very often due to its extreme remoteness.
Willis and his fellow team members, which also included Taranaki farmers Terry and Heather Nelly who are Willowbank supporters, were at Chalky Bay to install and then retrieve birdsong and trail camera equipment used to try and find the South Island kōkako.
The cannon find has followed a tradition for the team of making great discoveries while searching for something completely different.
“Fiordland is just full of mysteries, there is so much going on there that no-one knows about,” Willis said.
Willis said team members were now waiting for the Ministry of Culture and Heritage to get back to them about how to go about retrieving the cannon. It had been too heavy to lift into their helicopter when they found it.
He said Willowbank hoped to obtain custodianship of the cannon and display it.