"They are certainly capable of learning and some of the sharks have learned that when they hear a boat in those particular places they come up and check them out."
Mr Duffy said recent findings from Australia showed sharks had learned where and when cage diving boats were operating and arrived early to wait for them.
But he said cage diving in Stewart Island was still at a fairly low level compared to Australia and South Africa, and sharks would have already been used to scavenging around fishing boats.
Commercial fisherman and charter operator Brett Hamilton said sharks were becoming "very bold, and actually seeking food from the boats".
The change in behaviour was concerning for paua divers and amateur divers, who were most at risk.
"It hasn't happened yet but it's only a matter of when, not if. I can't see this behaviour of having sharks associate food with boats coming to anything good."
Mr Hamilton said cage diving had an economic spinoff for the island, but the impact on other water users needed to be considered.
Local Richard Squires said in 40 years of fishing off Stewart Island, it was only in the past five or six years he'd seen sharks approaching boats.
In one case a 3.6m shark attached a buoy on the back of his boat, he said.
Sharks also followed boats, and he worried about them being drawn into the harbour where children were swimming.
"You never used to worry about these things in the past, now you do."
However, Shark Dive NZ director Peter Scott said sharks have always been there, and he hasn't seen a change in behaviour in his seven years of cage diving.
"It's nothing new, it's just that I'm new on the block," he said.
About 10 to 15kg of berley was used in a cage dive, he said, which was less likely to attract sharks than the half-tonne of offal dumped by commercial fishermen.
Fishing operators cleaning their catch at the entrance to Half Moon Bay were more likely to attract sharks into the harbour, he said.
Mr Scott said he estimated shark diving contributed $100,000 to the Stewart Island economy every season.
Sharks are typically in Stewart Island waters from November to May, with numbers peaking around late March and early April.