Vehicles affected by the recall are certain four-cylinder Accord cars for model years 2005 to 2010; the CR-V for model years 2007 to 2010; and the Element for model years 2005 to 2008.
Without the updated software, the automatic transmission secondary bearing could be damaged if a driver quickly shifts between reverse, neutral and drive positions, which may be done when trying to dislodge a vehicle stuck in mud or snow.
If the bearing gets damaged, it could cause the engine to stall or lead to difficulty engaging the parking gear.
Honda says the software update will ease the transition between gears to reduce the possibility of damage.
No injuries or deaths related to the condition have been reported.
Honda says customers will begin receiving notification of the recall on August 31, and should then take their vehicles to an authorized dealer.
The car maker also announced that it will recall about 1.5 million vehicles in the U.S., and another 760,515 vehicles in China, to update the automatic transmission control software.