The whale was dragged in on the front of a cargo vessel, a strandings investigator said
Two thirds of the fin whale's carcass, measuring 10m (33ft), was found on RSPB land near Harwich.
It was dragged in on the front of a cargo vessel but experts believe it may have been hit by another ship.
The decision has been taken between scientists and landowners to leave the remains in place as it is not considered a public health hazard.
The body was found last week on private land with no public access, said Rick Vonk, site manager of the RSPB Stour Estuary site.
"We're scratching our heads as to how this happened," he told the BBC.
"Fin whales are a very northerly species. We don't know what it was doing to get hit, presumably by a container vessel.
"It's unfortunate this has happened - we like to see live whales rather than dead ones," he added.
Rob Deaville, project manager of the Cetacean Strandings Investigation Programme (CSIP), was called out to examine the whale.
"Leaving it in place was the most pragmatic decision in this case, as trying to remove it would damage the local habitat," he said.
Mr Deaville said fin whales were prone to ship strikes, but his project had only been involved in two other cases of fin whales brought into harbour on the front of vessels over the last 25 years.
He said there are about 600 strandings in the UK each year, of which two or three are fin whales.
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