No, they're actually slightly more expensive than a regular taxi. The growth limiter for Uber in Japan is the strict regulation around transportation vehicles, partly due to the government's close ties with the taxi industry, and partly because I think the government wants to disincentivize car use in its bigger cities (this makes a lot of sense, since in Japan's large cities, public transportation is quite good).

Because of this, any kind of commercial activity using a motorized vehicle is highly regulated - services like UberX are impossible to launch in Japan. Even for food delivery, delivery drivers all ride bicycles.