The giraffe was dissected after being put down in front of a group, including young children.
Bengt Holst, scientific director at the Danish zoo, has defended Marius's destruction, saying that the giraffes at the zoo bred very well, and where this was the case giraffes had to be selected to ensure the best genes were passed down to ensure the animal's long-term survival.
He told the BBC it was a responsible practice on the part of zoos to manage their animal populations to ensure they remained healthy, with some 20-30 animals put down at Copenhagen Zoo in a typical year.
Stine Jensen, from Denmark's Organisation Against the Suffering of Animals, said Copenhagen Zoo was behaving unethically.
"This situation should not have occurred at all. It just shows that the zoo is in fact not the ethical institution that it wants to portray itself as being, because here you have a waste product - that being Marius.
"Here we have a zoo which thinks that putting this giraffe down instead of thinking of alternatives is the best option," she said.