Authorities report that the incident occurred during an air-to-air refueling exercise.
Japan’s defense ministry reported that of the seven missing service personnel, it had found two.
The collision occurred between an F/A-18 Hornet fighter jet and a KC-130 Hercules, and has spurred the call for investigations of military capability.
Congressional leaders have said the recent state of military accidents is a “crisis.”
Aviation accidents have skyrocketed in the last few years, increasing at least 40 percent and killing 133 service members.
Many people blame the sharp cuts the military was subjected to under Obama, such as deferred modernization and old equipment, while others have speculated that these incidents are not accidents.
They point to the strange sonic technology that has struck a number of U.S. Ambassadors, and also the strange sea-going collisions that have taken place over the past 16 months.
One of the crew is in a stable condition at Marine Corps Air Station Iwakuni, while the second was discovered about 10 hours after the collision.
That person was taken aboard a Japanese military vessel, the ministry said, however, no other details about the second Marine were shared.
“We plan to keep at it all through the night,” Katsutoshi Kawano, chief of the Japanese Self-Defence Forces’ Joint Staff, told a news conference.
Reuters reported, “People in a Tokyo hospital waiting room fell silent as news of the crash came on television, with one woman whispering to another, “This is so scary.”
“The incident is regrettable, but our focus at the moment is on search and rescue,” Japanese Defence Minister Takeshi Iwaya stated during a news briefing. “Japan will respond appropriately once the details of the incident are uncovered.”
U.S. Ambassador William Hagerty thanked Japan’s military for their search-and-rescue efforts, saying, “My heart goes out to the families and colleagues of Marines involved in this tragedy,” at an event at Waseda University in Tokyo.
“They risk their lives every day to protect Japan and to protect this region and sometimes they pay the greatest costs. So I want to emphasize this security alliance that we have is critical and it is moving forward to the right direction,” he added.