Japan used the Wabun code, a variant of morse where each combination of dots and dashes equals not a letter, but a kana. This was used by both military and domestic vessels... of course for military use a sent message may have been in code... the infamous "Climb Mount Niitaka", signalling the go-ahead for the Pearl Harbor attack, would be an example.

The US military understood the Wabun code, but it was the underlying security codes used that were hard to crack. It was JN-25 that was broken early in the war that allowed the US Navy to "read Japanese mail," and led to the ambush at Midway.

But it was still based on the Wabun code.