About 726,000 polyurethane condoms were loaded into a container at a factory in Malaysia, said Sagami Rubber Industries, founded in 1934 as the first condom maker in Japan.
But the shipment was empty when it arrived at the company's main plant in suburban Tokyo last week, company spokesman Norinari Wakui said, adding that the lock on the container had been replaced before it left port in Malaysia.
The items, which are 14 percent thinner than conventional products at 0.02 millimetres, are worth 120 million yen (1.5 million dollars) at Japanese retail prices, he said.
"This has never happened to us before and we are very perplexed," Wakui told AFP. "We are not certain if it was of a premeditated nature."