The normally white bears at the Higashiyama Zoo and Botanical Gardens changed colour after swimming in an algae-filled pond.
Zoo official Masami Kurobe said the green polar bears had sparked concern amongst visitors about whether the animals were sick or carrying mould.
High temperatures in July and August and less-frequent water changes because of the zoo's conservation efforts had caused an algae growth in the bear pond and safety moat.
Mr Kurobe added that the algae enters hollow spaces in the bears' fur and was hard to rinse off.
The bears are expected to return to their natural colour when the algae growth subsides in November. (AP)