The country's "Diskrimineringsombudsman" (DO) found that the pool's decision was illegal and that anyone identifying as transgender should be permitted to swim in public pools without having to cover their breasts.
Local media have said that the ruling, a copy of which has been seen by AFP, could set a precedent and mean that all women wanting to swim topless will be free to do so - regardless of their gender identity.
DO spokesman Clas Lundstedt, however, told AFP: "The decision is for a particular situation, it does not enact a rule that applies to all pools."
The DO said the complainant was barred from a Stockholm pool because they insisted on wearing only swimming trunks to use the facilities.
The management treated the pool user as a woman while they wanted to be identified as transgender.
Carina Engström, manager of the Liljeholmsbadet pool in the Swedish capital, said that the DO's decision might upset the sensibilities of users of different cultures or religions.
"Some women bathe in a full swimming costume," she told the TT news agency.
Other local pool managers have raised concerns about the risk of possible sexual assaults in swimming baths if women are allowed to swim topless with several recent cases firing debate on the issue in the media and online.
