Hundreds of the insects swarmed in Piazza Fiume, a square located close to the Corso d'Italia.
Transport workers and local police cordoned off the area for several hours until firefighters and animal experts were able to deal with the bees later in the day. Video footage showed disconcerted residents and tourists passing by.
Photos shared on social media showed the impromptu colony, with the bees swarming around a railing leading to a subway stop.
The city has experienced several problems due to unwelcome visitors from the animal kingdom.
Health Minister Beatrice Lorenzin has said the rising number of rats in the capital is an "extremely serious situation" after several cases of bites from rats in the city's parks were reported. Lorenzin also warned of infections carried by seagulls and cockroaches, the presence of which has also increased.
Wild boar sightings have also risen in recent years, and the city said it was considering options such as sterilization to deal with the animals, after a man died when a boar collided with his scooter at night.
But some locals took to social media to ponder whether there could be another reason behind the incidents, joking that Rome seemed to be experiencing its own version of the ten biblical plagues.
Oggi a Roma, dopo topi, conghiali e gabbiani sono arrivate le api. A quando le cavallette e le rane?— Simonetta Picasso (@kunta61) June 6, 2017
Today in Rome after rats, wild boar and seagulls, the bees have arrived. So when are the locusts and frogs coming?
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Rome mayor Virginia Raggi. Photo: Andreas Solaro/AFP