Digging out the whale in wet weather has been mucky work. (CBC)

Scientists digging up a blue whale in western P.E.I. say they believe they have discovered what killed it before it washed up on the beach 20 years ago.

The whale came ashore near Tignish in November 1987 and was buried near the shore. Scientists from the University of British Columbia have been digging it up for display at a new biodiversity museum in Vancouver.

Scientists hoisted the last and largest bones, parts of the skull and jaw, from the mucky hole on Wednesday and had their first good look at them.

"There's an awful lot of damage on this side of the skull. Something very hard had to have smashed into it," said team leader Andrew Trites.

"Our best guess is that it was more than likely a ship. Probably hit this whale on the side of the head and killed it instantly."

The jaw of the blue whale, 7.6 metres long and weighing about 1.5 tonnes, is the largest bone of any creature that has ever lived. (CBC)

Finding the cause of death brought a grim satisfaction to the dig team. Blue whales are an endangered species, with just a few thousand surviving.

The damage from the death blow is not the only problem with the skeleton. The team has pulled more than 500 bone fragments from the hole. Blue whales only have between 160 and 180 bones.

Trites said he believes most of the damage came from the heavy equipment used to bury it in 1987.

"We know that when the whale was buried, it was fairly roughly handled, and we found a lot of damage to the overall skeleton," he said.

Piecing the bone fragments back together will be nearly as big a job as getting them out of the ground.