I have a relative who served as 1st class torpedoman and gun captain during the war. He said they usually would stop and search small shipping in the Phillipines area. If carrying controband the crew would be ordered off and they would sink it. If it had a radio, it was down. If it was armed, the crew was not afforded the courtesy noted above...
The Japanese commandeered many of these small ships to run supplies from island to island...
Edit: If it was native and not carrying anything that would obviously help the Japanese, they would let it go. It seems tp me that how the situation was handled was up to the discretion of the submarine commander...
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