"We think it is a pity that we have to take it away because the Berliners' response has been brilliant," said Bjoern Jettka, a spokesman for the environmental group.
He said large crowds had gathered to look at the 17-meter (55-feet) -long mammal that was laid on a trailer in the snow in front of the embassy from Wednesday night to Thursday afternoon in a protest at Japanese whale hunting.
The whale, which was between 10 and 20 years old, was brought to Berlin by the environmental group after it was found beached near Wismar on Germany's Baltic coast on Saturday.
They had hung a banner over it stating: "Science does not need harpoons."
Greenpeace activists said the whale came from the North Atlantic and appeared to have beached after hunting for herring and being trapped in shallow waters in the Baltic.
They began transporting the whale to the maritime museum at Stralsund in northeastern Germany where it was due to be dissected on Friday.
The director of the museum, Harald Benke, said he was initially angry to learn that Greenpeace had "kidnapped" the whale by taking it on a detour to Berlin, but later realised that the protest had served a purpose.
"This whale in Berlin spoke more loudly against whale hunting than many words," he said.
Greenpeace is leading an international campaign against whale hunting by the Japanese, and has recently been involved in high-seas confrontations with Japanese harpoon ships in the Antarctic Ocean.
The International Whaling Commission imposed a moratorium on commercial whaling in 1986 but Japan has continued hunting for what it calls scientific research.
Japan, however, makes no secret of the fact that the meat from the hunt winds up on dinner plates.
The Japanese embassy in Berlin on Thursday defended whale hunting, saying scientific research was essential for the survival of the species.