The fault, according to Toyota, is a software issue that could cause the cars to not enter a designated failsafe mode in certain situations associated with the hybrid powertrain.
'If this occurs, the vehicle could lose power and stall.
Toyota will send recall notifications via first-class mail when the necessary software updates are available.
In a statement, the company said that some vehicles could fail to switch to a "failsafe" driving mode, increasing the risk of potential crashes.
Toyota also added there was no current data to suggest how many similar incidents had occured outside of Japan. Toyota did not say how many customers reported stalling incidents, whether there were accidents, or when customers could bring in their cars for fix.
A Toyota dealer in California highlighted the issue earlier this year when it sued Toyota over what it claimed was an inadequate fix for the safety problem.
About 1.25 million cars are affected in Japan, 807,000 in the U.S., 290,000 in Europe and 3,000 in China.
Three malfunctions related to the issue were reported in Japan, with no accidents caused.
This is not the first time Toyota's hybrid cars have been recalled, with the affected cars previously suffering problems in 2014 and 2015.
Prius hybrids can stall without warning due to a software error that won't detect powertrain problems and correspondingly won't place the vehicle in a "limp home" mode that restricts speed.