According to the US Navy, the two pilots on board have been rescued and are in good condition.
The fighter, which was based out of US Marine Corps Air Station Iwakuni in Japan's Yamaguchi Prefecture, crashed during a training exercise at around 11:45 am (02:45 GMT).
The American F/A-18 multirole fighter crashed "due to engine trouble," Osamu Kosakai, a spokesman for the Japanese defence ministry's Okinawa Defence Bureau said.
This is not the first incident involving a USS Ronald Reagan aircraft lately. In October, immediately after taking off, a US Navy MH-60 helicopter crashed onto its deck, causing several casualties.
In particular, residents and local authorities have demanded the withdrawal of Marine Corps Air Station Futenma from the prefecture, but it was previously decided to transfer it to the Henoko area, also in Okinawa.