One serviceman has already been rescued and is thought to be in a stable condition, Takeshi Iwaya told reporters.

"US military and the Japanese Self-Defense planes and vessels are searching for those still missing... I hope all the members will be rescued safely as soon as possible," Iwaya added.

The marines were conducting "regularly scheduled training" when the crash occurred around 2am local time, the 3rd Marine Expeditionary Force said in a statement.

The F/A-18 fighter jet with two crew onboard and a KC-130 refuelling tanker with five crew -- crashed into the sea around 100 kilometres (60 miles) off the cape of Muroto in south-western Japan, Iwaya said.

The crew member rescued had been in the fighter jet, the minister confirmed.

Japan's Self-Defense Forces had deployed nine aircraft and three vessels for the search, he said.

"We are thankful for the Japan Maritime Self-Defense Force's efforts as they immediately responded in the search and rescue operation," the Marines said.

A spokesman for the Japanese coastguard said six vessels and an aircraft had been dispatched separately to assist in the rescue efforts.

There are few details about the circumstances of what the Marines described as a "mishap" and an investigation is underway.

The US military has about 50,000 troops stationed in Japan and accidents are not uncommon.

In November, a US navy fighter jet crashed into the sea off Japan's southern island of Okinawa and its two crew members were rescued alive.

And in November 2017, a C-2A "Greyhound" aircraft with 11 people on board went down in the Philippine Sea -- eight were rescued and the search was called off for the remaining three after a two-day search.

The US military has also experienced difficulties with its Osprey helicopters, with several emergency landings, a deadly crash and a piece of the chopper falling on the grounds of a Japanese school.

Those incidents have stoked tensions between close military allies Washington and Tokyo and led to protests against the deployment of Ospreys by residents living near US bases.

Iwaya said the incident was "regretable but at this point we are doing our utmost to rescue those still missing."

"Later, if we get to know the details of the accident, we will take appropriate measures," added Iwaya.

He said that there was no information that any passing vessels were affected by the crash.