Blue whales are the largest animals in the world, each measuring the length of three school buses.
DFO researcher Jack Lawson said the deaths are a serious blow to an endangered population of about 250 animals.
"It's horrible and it's so disappointing for us, because the department is working hard to develop a recovery plan for the species," he told CBC.
"We are trying to monitor man-made threats like seismic or vessel strikes and that kind of thing, and then to have a natural event like this happen, you really have no control over it and it's pretty shocking."
On Tuesday, CBC reported that a dead sperm whale washed ashore near Trepassey, on the island's Avalon Peninsula.
Lawson said if the wind changes direction, the whales can be left in the ice with nowhere to turn.
"It's like putting a lid back on a cup — it just traps the animals in there, and if it keeps pushing it can kill them."
Last week, Lawson flew over the dead whales. He hopes to get a closer look at them later in the spring season.
Lawson said there have been reports of whales trapped and dying in sea ice in the area dating back to the mid-19th century.
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