The dead whale was removed from the ship at around 10am and towed to a location where it could be properly disposed of.
It is the second such incident to happen in Lisbon’s docks in recent times.
On 28 August another whale was killed after colliding with a cargo ship that later also docked in Alcântara with the carcass still stuck to it.
The carcass was removed and towed to Algés, where it was incinerated on land.
Lisbon Port Commander Malaquias Domingues said a team from the Nature and Forest Conservation Institute comprising biologists went to the port to conduct tests on the dead animal.
It was then towed to Algés “where there is specific equipment” to haul it onto land and properly dispose of it.