There were no immediate reports from authorities of damage or casualties
The auto giant said it would call back about 2,800 Mirai vehicles made between November 2014 and December 2016 to repair the defect.
Toyota launched Mirai -- which means "future" in Japanese -- in late 2014 as it looked to push further into the fast-growing market for environmentally friendly cars.
Mirai was its first mass-market hydrogen fuel-cell car, after Toyota scored a win with the top-selling Prius hybrid, which combines a regular engine and rechargeable electric battery.
Separately, Toyota on Wednesday launched a new plug-in model of its Prius, after the first version sold poorly following its 2012 release.
The new model can run in electric-only mode -- unlike the original Prius -- at higher speeds and longer distances than the previous version, Toyota said.
Fuel cells, meanwhile, work by combining hydrogen and oxygen in an electrochemical reaction, which produces electricity. This can then be used to power vehicles or home generators.
But a lack of hydrogen refuelling stations has been a major hurdle to bringing fuel-cell cars into the mainstream.
The Mirai was launched with a relatively expensive 6.7 million yen ($58,000) price tag.
There were no immediate reports from authorities of damage or casualties
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