Zoo workers found the sea lion, named Holly, dead in her pen on Friday morning.
A spokeswoman for the city of Dortmund told The Local that at first officials had thought it was an accident, but the autopsy announced on Monday showed that there was "evidence of possible foul play".
There were signs of a blow to her skull and she was also missing three teeth. The autopsy further reported that the death could have been caused by stress induced by the abuse.
Zoo staff found a hole in the zoo's fence near the sea lion enclosure, which could indicate that someone broke in the night before the 21-year-old sea lion was found dead.
"The employees who worked directly with her are very sad, and the zoo as well," Zoo director Frank Brandstätter told The Local.
Brandstätter described Holly as "very sweet and sporty". She also had one young pup and other grown children.
"She was very popular at the zoo," Brandstätter said.
The director added that there had been break-ins at the zoo before, but nothing like this case.
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Dortmund police told The Local that it was still unclear whether the person who broke in was from the zoo or not, though the hole in the fence supported a break-in.
Brandstätter emphasized that he did not believe a staff member was responsible.
Police are asking any witnesses who may have seen anything or have any information about the sea lion's death to call 0231-132-7441.