Biologists from the New England Aquarium examined and marked the whale found early Sunday, WCVB-TV, Boston, reported.
They said they were not yet sure how the whale died, but had discerned a lot of bruising and pressure lines -- a sign something may have been wrapped around the whale.
"We don't know," said Tony LaCasse, a spokesman for the aquarium. "We've only been able to look at a small portion of the body so far."
LaCasse said the animal likely died of natural causes, disease or a unique medical problem, such as being struck by a vessel.
Authorities said finding a dead whale in Boston Harbor is a rarity, The Boston Globe reported.
"It's not rare to see a whale in the Boston Harbor, but it's rare to see a dead whale in the Boston Harbor," said Brian Fleming, command duty officer with the U.S. Coast Guard in Boston. "The majority of these cases happen out to sea."
Authorities will wait for the carcass to wash up so they can examine it and then dispose of it.