Flames were seen under the wing and fallen parts were scattered at sites near the western city of Komatsu.
No-one was injured in the incident and the plane landed safely.
It is the second time in three months that officials have suspended F-15 flights.
The 155-kg (150lbs) tank, which was empty, and parts of a dummy missile came free and fell from the plane as it was nearing a field for landing. The debris fell on 10 locations, including a sewage plant, officials said.
"We take this accident very seriously," Gen. Shigeru Iwasaki, the head of Japan's air forces, said at a news conference on Friday. He said the cause was under investigation.
In July, the fleet was grounded after a plane crashed into the East China Sea. The pilot, though presumed dead, is still listed as missing and no cause of the accident has been declared.
Japan Air Self-Defence Force officials said that all missions except emergency scrambles were suspended and will last until the safety of Japan's 202 F-15 fighters has been confirmed.
The latest incident comes as Tokyo is seeking to replace its aging fighter jets. It is considering both US-designed aircraft and the Eurofighter Typhoon in a deal expected by the end of the year and worth more than $8bn.