With visible blood, bruising and pressure lines, Aquarium spokesman Tony said that its most obvious injuries could be caused by something wrapping around the whale.
'Seeing blood is significant, a lot of times in most whale deaths you won't see blood,' Mr Lacasse told NECN.
Joey Brancato, a local fisherman, said the scene was extremely unnerving as he filmed it floating off Dear Island around noon on Sunday.
'We thought it was a capsized boat at first so went over to take a look and see if we could help out until we realized the fin was out of water and we realized it was a finback whale,' he told NECN. 'I was freaking out; I've never seen a whale that up close.'
After allowed to float freely down the Harbor, Officer Simpson said the whale beached at Long Island, in the middle of Boston Harbor.
Before its beaching officials told NECN that where it washed ashore would make it the landowner's responsibility to get rid of.
Long Island today is mostly used for social service programs including a homeless center and various recovery programmes.
A necropsy is now planned on the whale to determine its cause of death.
The finback is the second-longest whale in the world behind the blue whale.
It can reach about 70 feet and weigh up to 70 tons.
Experts believe the whale had been dead for about three days before found.