I doubt those bonds were counterfeit because of their large denominations. Who would deal with them without first examining them and their history. If the bonds were worth 10 million each instead of 500 million, perhaps they could move them without detection.

They might have been real but stolen, since if the Japanese really wanted to move bonds around, all they need do is use the diplomatic pouches of their top diplomats who usually pass through customs in any country without a hassle.