TOKYO (AP) _ Following inspections on Boeing 747s ordered by the Japanese Transport Ministry last week, Japan Air Lines today reported minor faults in tail sections of three of the 24 jumbo jets it has checked so far, ministry officials said.

In a separate development, the national police said Wednesday they will investigate possible criminal negligence in the Aug. 12 crash of JAL Flight 123, which killed 520 people and led to the JAL inspections.

Officials of the Airworthiness Division of the ministry's Aviation Bureau today said JAL reported ''minor findings,'' or minor faults, on the planes, and said the ministry would announce results of JAL's inspection later.

Airline spokesmen refused comment on the Airworthiness Division's findings, saying it was up to the ministry to make them public.

However, Japanese press reports said a JAL maintenance crew found a crack in the rudder hinge of one ''older'' plane with more than 15,000 takeoff- landing ''cycles.'' The reports said the aircraft was a standard 747 leased by JAL to its wholly-owned subsidiary, Japan Asia Airways, which primarily serves Japan-Taiwan routes.

Kyodo News Service and the mass circulation Asahi Shimbun said JAL maintenance crews also found ''scratches'' on the surface of aft pressure bulkheads - the dish-shaped aluminum wall that helps contain pressure inside the cabin - apparently made during assembly or regular maintenance work.

A bulkhead rupture has been suggested by some investigators as a possible cause of the crash of JAL Flight 123, a 747SR, or short-range jumbo jet. The crash was aviation's worst one-plane disaster.

The crash occurred after the plane's tail fin disintegrated and its hydraulic systems failed in flight, sending the jetliner on an uncontrollable course that ended when it plowed into a ridge on Mt. Osutaka, 70 miles northwest of Tokyo.

The Transport Ministry today began its own series of on-the-spot inspections of JAL's maintenance centers.

Shiro Oshima, head of the agency's technical department, and 15 inspectors visited Tokyo International Airport at Haneda, where they examined maintenance and service reports and acquired ''background'' information on the service performance on JA-8119, the jet that crashed, bureau officials said.

The government inspection was to focus on repairs that were done following a 1978 incident in which the same plane scraped its tail on the runway on landing at Osaka. In making repairs, technicians of the Boeing Company, makers of the 747, replaced portions of the pressure bulkhead that divides the pressurized cabin from the non-pressurized tail section.

Members of Oshima's team also conducted inspections at JAL's maintenance center at the New Tokyo International Airport at Narita, the main airport for international flights. It was the sixth on-the-spot inspection in the last decade, four of which involved JAL, Airworthiness Division officials said.

At the crash site atop 5,408-ft. Mt. Osutaka, ministry and police officials Wednesday arranged for the airlifting of pieces of the plane wreckage considered important to the investigation, police said.

Ministry officials said they would bring pieces from the tail fin, the tail cone section and the pressure bulkhead to a ''suitable location'' for detailed metallurgical analysis by specialists from the government's Science and Technology Agency.

Joining the investigations at the site Wednesday were Boeing accident investigator John Purvis and officials of the U.S. National Transportion Safety Board and the Federal Aviation Administration.

U.S. and Transport Ministry officials also began mapping out the wreckage and conditions of the victims for a detailed study of crash conditions, Japanese officials said.

As of Wednesday, 490 bodies had been recovered and 448 identified, Norie Yoshizawea, a spokeswoman for Gunma prefectural police, said. A police officer at Uenomura, headquarters for the operation, denied press reports that the search for bodies was to be terminated on Friday. He said 2,200 workers were still at the crash site, and were conducting a ''tree-to-tree search'' for remains of victims.