Japan's transportation ministry said Toyota had reported three malfunctions locally related to the issue, but no accidents.
The car giant last month issued a recall for 1.03 million cars globally over an issue related to wiring that could cause fires in vehicles.
Raising concerns
"We can't assess the impact of the recall immediately as we first need to analyse details of the problem, but the latest recall at least raised concerns as Prius is Toyota's leading brand," said Satoru Takada, an analyst at TIW, a Tokyo-based research and consulting firm.
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But the news had little impact on Toyota shares, which ended marginally lower.
Toyota has sold more than 12 million hybrid gasoline-electric vehicles globally, including the Prius, since 1997.
In 2016, it announced the recall of 3.37 million vehicles globally over problems with airbags and a fuel emission control unit.