The Department of Fisheries and Oceans is investigating two vessels under the Marine Mammals Act.
CBC News went on a ride-along last week as a DFO team set out to do research on whales. But they had to stand down after two boats started chasing the mammals.
DFO scientist Jack Lawson and his team were working with the whales when a couple of boats, including a tour boat filled with tourists, moved in and prevented them from continuing their research.
Lawson's crew moved away.
"They're being chased by a couple of boats already so why add to the mix?" Lawson said, concerned by what he saw.
"[The whale] was changing its course and moving faster so it had to stop what it was doing ... maybe looking for food, and instead was trying to find a way to move away from the boats and the motor noise." he said.
DFO can't comment on the incident because it's under investigation.
Tracking the whales
Lawson and his team are tracking the whales to see if the numbers coming here to feed on caplin are increasing or declining, and whether endangered species are passing through the north Atlantic Ocean.
Lawson also photographs whale tails, otherwise known as the fluke.
"Ideally, what we want to get is a photograph of the underside of the fluke, which is much like a fingerprint," said Lawson. "No two humpback whales have the same pattern on the underside of their flukes."
The fluke also shows if the whale has been attacked by a killer whale, or damaged by fishing gear.
Lawson and his team also take biopsies of whales. They have a special permit to pursue the whales and get close enough to obtain tissue samples.
"We take the crossbow and shoot it at the animal," said Lawson. "It goes in only as far as this rubber stopper and pops back out and we get a little tissue sample."