In this mode, the car's speed is limited at 30-45MPH, which prevents further damage to the engine but allows the driver to vacate the road.
In rare cases they might not enter a "failsafe" driving mode, lose power and stall, the company warned. The carmaker stated that no actual accidents have been recorded so far.
The recall applies to 1.25 million vehicles in Japan, 807,000 in the U.S., 290,000 in Europe and 3,000 in China, with the rest across the globe.
When that happens, "the vehicle could lose power and stall". This could cause the vehicle to stall, which could increase the risk of a crash when driving at high speeds.
Toyota is now in the process of recalling around 2.4 million cars worldwide over fears that a faulty component could cause some vehicles to stall without warning.
Toyota said it had received three reports from Japan by the end of September that related to the problem and it reported them to the transport ministry.
A total of 744 Prius cars produced between Oct 2008 and Nov 2014 are affected in this recall.
"Due to inappropriate programming in the airbag electronic control unit (ECU), a fault may be erroneously detected during vehicle startup which would disable one or more of the sensors used to detect crashes", Toyota said.
In a statement, Toyota said the cars had already been involved in previous recalls in 2014 and 2015, but "the remedy conducted then did not anticipate the new condition identified in this recall".
Toyota shares ended slightly down on Friday.
Toyota has sold more than 12 million hybrid gasoline-electric vehicles globally, including the Prius, since 1997.