The drills—dubbed Keen Sword—will continue until December 10.
Washington has deployed more than 10,000 troops, 20 warships and 150 aircraft to take part in the maneuvers.
Tokyo recently invited South Korean military officials to observe the exercises.
The exercises come several days after an exchange of artillery fire between the two Koreas.
However, US and Japanese officials claim the drills were planned before the Korean clashes.
The developments come days after Japanese on the southern Island of Okinawa re-elected incumbent governor Hirokazu Nakaima, who wants an end to the American military presence in the island.
Nakaima, who wants the US Futenma airbase off Okinawa altogether, defeated his opponent who agreed to relocate the base to a less crowded area on the island.
Futenma hosts about half of the US troops in Japan as the row over the airbase has given new headaches to Japan’s Prime Minister Naoto Kan.
Futenma has provoked a wave of angery protests in the country, with the nation demanding a complete removal of the airbase off Okinawa, which has been under the US command since the end of World War II.