According to USA media reports, there were two crew on the fighter jet and five personnel on the tanker plane.
The Marine Corps said Japanese search-and-rescue aircraft immediately responded to aid in recovery efforts.
The incident occurred after the planes took off from Marine Corps Air Station Iwakuni in Japan, Marine Corps officials said in a statement.
A KC-130 midair refueling a tanker and an F/A-18 fighter jet, which was being refueled, were involved in what the military called a "mishap".
A US Marine Corps F-18 fighter takes off from the North Atlantic Treaty Organisation military base in Aviano, Italy. Search and rescue efforts are ongoing to find the aircrafts, along with the six missing military personnel.
U.S. Marine Corps Air Station Iwakuni is located in Iwakuni, Yamaguchi Prefecture, and is home to the sole forward-deployed Marine squadron of F-35 stealth fighter jets.More news: CNN Repeatedly Attacks Trump For Paying Respects To George H.W. Bush
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The Marines did not release details of the punishment given to the pilots because the discipline was administrative in nature, according to The Hill.
Officials who spoke to Reuters on condition of anonymity were unsure precisely how the mishap occurred but none suspected foul play.
The circumstances of the mishap were under investigation and no other information was available, according to the statement.
However, refueling is a unsafe operation, Baker said.
More than 50,000 US troops are based in Japan under the bilateral security pact.