JN-39 was replaced by JN-40, which was originally believed to be a code super-enciphered with a numerical additive in the same way as JN-25. However, in September 1942, an error by the Japanese gave clues to the codebreakers at the FECB, Kilindini. In fact, the code was a fractionating transposition cipher based on a substitution table of 100 groups of two figures each followed by a columnar transposition. By November 1942, they were able to read all previous traffic and break each message as they received it. Enemy shipping was thus trackable, enabling Allied submarines to successfully attack it.
Read more about this topic: Japanese Naval Codes