The animal, which was floating in the surf, seemed to have been injured before its death and a part of its body appeared to be bloated.
Hundreds have flocked to the beach to catch a glimpse of the unusual sight.
Initial reports suggested it may be a minke whale but Suzanne Beck, a scientist with the Agri-Food and Biosciences Institute in Northern Ireland, has cast doubt over the species.
The minke is the smallest of the baleen whales found in UK waters, measuring 22 to 32 feet when fully grown, with females usually growing to be slightly bigger than males.
It is also the most commonly spotted type of whale around the Northern Ireland coast but Ms Beck believes the one which washed up on Monday may be a juvenile fin whale, as it does not have a distinctive white band across its body, which is indicative of a minke whale.
Minke or Sei whale beached on Portstewart Strand this morning - the red bit is its bloated tongue I'm told pic.twitter.com/utVmgs4cVGMs Beck said she will be going to the site on Tuesday to collect samples and determine what happened to the mammal.
โ Peter Lynas (@peterlynas) October 5, 2015
"Its injuries may have happened after death. It could have been washed up on rocks," she said.
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