The problem surfaced in January in Kanagawa Prefecture southwest of Tokyo, and Apple reported the problem to the ministry in March. No one was injured, the official said. Other details weren't available.
Apple Japan did not contest the ministry statement but declined further comment. Nano players are sold all over the world, and it was still unclear where else besides Japan the suspected model was sold, said Masayoshi Suzuki, an Apple spokesman in Tokyo.
The ministry has instructed Apple Japan to find out the cause of what it is categorizing as a fire and report back to the government.
The iPod was assembled in China, but it was unclear who made the lithium-ion battery, the ministry official said.
Lithium-ion batteries have been blamed for a series of blazes in laptops recently that have resulted in massive global recalls.
The ministry said Apple has shipped about 425,000 iPods of the same suspected model were shipped into Japan. It was unknown how many have been sold and how many might still be in stores.
Shipments of the model began in September 2005 and were discontinued after September 2006, the ministry said.
The iPod has been the symbol in recent years of the successful fashionable image of Apple. But its sales momentum may be gradually running out of steam.
Apple sold 22.1 million iPods during the holiday quarter ended Dec. 31, fewer than the 25 million iPods analysts had expected it to sell. That's raising fears that the company, based in Cupertino, Calif., may suffer as it tries to convince consumers to buy higher-end iPods — a key part of its strategy.
The batteries in Apple products have had some problems in the past, largely about wearing out, not about being prone to fires.
In 2006, Japanese electronics and entertainment maker Sony Corp. apologized for the troubles it had caused consumers through defective lithium-ion batteries that had equipped Sony laptops and products by Dell Inc., Apple, Lenovo and other major manufacturers.
The Tokyo-based company recalled about 10 million batteries following reports of some computers using Sony power packs overheating and bursting into flames.
The lithium-ion battery is considered an overall good technology because of its ability to furnish power in relatively small sizes, although its suspected tendency to catch fire is a major reason Toyota Motor Corp. and other automakers are being cautious about using it in ecological cars.
Toyota's Prius gas-electric hybrid uses a different kind of battery, and the switch in future green models to the lithium-ion battery will be seen as a considerable breakthrough.