The US Marine Corps on Tuesday confirmed the deaths of five soldiers who went missing after two US warplanes collided off the coast of western Japan, bringing the total death toll to six with only one survivor.

"I have made the determination to end the search and rescue operations for the crew of our KC-130J aircraft which was involved in a mishap off the southern coast of Japan and to declare that these Marine warriors are deceased," III Marine Expeditionary Force's Commanding General Eric Smith said in a Facebook post.

Smith added that "every possible effort was made" to recover the crew and that the flight data and cockpit voice recorders of the refuelling aircraft, which was carrying the five marines, "have not been located at this time, making it premature to speculate about wreckage recovery."

The US Marine Corps warplanes involved, the KC-130 and an F/A-18 jet with two on board, had taken off from Marine Corps Air Station Iwakuni, Japanese government spokesman Yasutoshi Nishimura said after the December 6 incident.

After the collision, two of the marines involved were rescued by the Japanese Navy. One died of his injuries while the other was in fair condition, the Corps said last week.

The planes were conducting "regularly-scheduled training" when the mishap occurred, according to a news release issued by the MIII Marine Expeditionary Force.

"It is not confirmed that aerial refueling was ongoing when the mishap occurred," the statement said, adding that the circumstances of the collision were under investigation.

There have been a series of accidents in and around Japan involving the US military. Thursday's crash comes less than a month after a US fighter jet went down off the southern island of Okinawa in mid-November and its two crew members were rescued.

Twelve sailors were injured in October after a US Navy MH-60 Seahawk helicopter crashed on the deck of the carrier in the Philippine Sea.

In October 2017, a US CH-53 helicopter went down near a residential area in northern Okinawa. None of its crew members were injured.