Marine Corps officials confirmed the incident, which they labelled a “mishap” but offered little information in a statement.
“The aircraft involved in the mishap had launched from Marine Corps Air Station Iwakuni and were conducting regularly scheduled training when the mishap occurred,” the Marine Corps Base Camp Butler statement read.
Search and rescue operations are underway for the marines who were on board the FA-18 jet and KC-130 refuelling tanker, which collided in the early hours of the morning.
The US Marine Corps says the aircraft were conducting regularly scheduled training about 320km off the coast of Iwakuni when the accident took place.
Japanese Self Defence Force search crews have so far rescued two of the seven marines.
The first rescued person had been on the FA-18 Hornet fighter jet, and was a in stable condition at Marine Corps Air Station Iwakuni.
The second crew member was found about 10 hours after the collision and brought aboard a Japanese military vessel.
No other details about the second marine were known, a ministry spokesman said.
“The incident is regrettable, but our focus at the moment is on search and rescue,” Japan’s Defence Minister Takeshi Iwaya said.
“Japan will respond appropriately once the details of the incident are uncovered.”
US officials speaking on condition of anonymity said they were unsure how the mishap may have occurred but none suspected foul play. An investigation had begun.
The Marine Corps said Japanese search-and-rescue aircraft immediately responded to aid in recovery efforts.
It was unclear if US military officials were also assisting with the search.
“We are thankful for the Japan Maritime Self-Defence Force’s efforts as they immediately responded in the search-and-rescue operation,” the Marine Corps said.
The crash is the latest in a recent series of accidents involving the US military deployed to and near Japan.
Last month, a US Navy FA-18 Hornet from the aircraft carrier USS Ronald Reagan crashed into the sea southwest of Japan’s southern island of Okinawa.
Its two pilots were rescued safely.
In mid-October, an MH-60 Seahawk also belonging to the Ronald Reagan crashed off the Philippine Sea shortly after take-off, injuring a dozen sailors.
Search and rescue operations continue for a KC-130 and an F/A-18 that were involved in a mishap off of the coast of Japan around 2:00 a.m. Dec. 6.
The circumstances of the mishap are currently under investigation.
Media can contact @IIIMEF at IIIMEFMEDIA@usmc.mil.
— U.S. Marines (@USMC) December 5, 2018