Japanese naval codes
The vulnerability of Japanese naval codes and ciphers was crucial to the conduct of World War II, and had an important influence on foreign relations between Japan and the west in the years leading up to the war as well. Every Japanese code was eventually broken, and the intelligence gathered made possible such operations as the victorious American ambush of the Japanese Navy at Midway and the shooting down of Isoroku Yamamoto in Operation Vengeance.
The Imperial Japanese Navy (IJN) used many codes and ciphers. All of these cryptosystems were known differently by different organizations; the names listed below are those given by Western cryptanalytic operations.
Red code 
This was a code book system used in World War I and after. It was so called because the American copies made of it were bound in red covers. It should not be confused with the RED cipher used by the diplomatic corps.
This code consisted of two books. The first contained the code itself; the second contained an additive cipher which was applied to the codes before transmission, with the starting point for the latter being embedded in the transmitted message. A copy of the code book was obtained in a "black bag" operation on the luggage of a Japanese naval attache in 1923; after three years of work Agnes Driscoll was able to break the additive portion of the code.
Blue code 
This was another code book system which succeeded the Red code.
The Fleet Auxiliary System, derived from the JN-40 merchant-shipping code.
JN-25 is the name given by codebreakers to the chief, and most secure, command and control communications scheme used by the Imperial Japanese Navy (IJN) during World War II (it was the 25th Japanese Navy system identified). Introduced in 1939 to replace Blue, it was an enciphered code, producing five-numeral groups for transmission. New code books and/or new superenciphering books were introduced from time to time, each new version requiring a more or less fresh cryptanalytic attack. In particular, JN-25 was significantly changed on 1 December 1940, and again on 4 December 1941, just before the attack on Pearl Harbor. It was the 1941 edition which was sufficiently broken by late May 1942 to provide the critical forewarning of the Japanese attack on Midway.
British, Australian, Dutch and American workers were cooperating in attacks on JN-25 well before Pearl Harbor, but because the Japanese Navy was not engaged in significant battle operations before then, there was little traffic available to act as raw material. Before then, IJN discussions and orders could generally travel by routes more secure than broadcast, such as courier or direct delivery by an IJN vessel. Publicly available accounts differ, but the most credible agree that the JN-25 version in use before December 1941 was not more than perhaps 10% broken at the time of the attack, and that primarily in stripping away its superencipherment. JN-25 traffic increased immensely with the outbreak of naval warfare at the end of 1941 and provided the cryptographic "depth" needed to succeed in substantially breaking the existing and subsequent versions of JN-25.
The American effort was directed from Washington, D.C. by the U.S. Navy's signals intelligence command, OP-20-G; at Pearl Harbor it was centered at the Navy's Combat Intelligence Unit (Station HYPO, also known as COM 14), led by Commander Joseph Rochefort. With the assistance of Station CAST (also known as COM 16, jointly commanded by Lts Rudolph Fabian and John Lietwiler) in the Philippines, and the British Far East Combined Bureau in Singapore, and using an punched card tabulating machine manufactured by International Business Machines, a successful attack was mounted against the December 1941 code edition. Together they made considerable progress by early 1942. "Cribs" exploited common formalities in Japanese messages, such as "I have the honor to inform your excellency" (see known plaintext attack).
The Purple cipher (also sometimes referred to as AN-1), used by the Japanese Foreign Office as its most secure system, had no cryptographic connection with any version of JN-25, or indeed with any of the encryption systems used by the Japanese military. Purple traffic was diplomatic, not military, and in the period before the Pearl Harbor attack the Japanese military, which effectively controlled Japanese policy, distrusted the Foreign Office and told it little. JN-25 traffic, on the other hand, was limited to military matters, mostly IJN operational ones, from which strategic or tactical information could sometimes be inferred. Nevertheless, decrypted Purple traffic was very valuable, especially later in the war,
This was a naval code used by merchant ships (commonly known as the "maru code"), broken in May 1940. 28 May 1941, when the whale factory Nisshin Maru II visited San Francisco, U.S. Customs Service Agent George Muller and Commander R. P. McCullough of the U.S. Navy's 12th Naval District (responsible for the area) boarded her and seized her codebooks, without informing Office of Naval Intelligence (ONI). Copies were made, in a clumsy way, and the originals returned. The Japanese quickly realized JN-39 was compromised, and replaced it with JN-40.
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.
A simple transposition and substitution cipher used for broadcasting navigation warnings. In 1942 the FECB at Kilindini broke JN-152 and the previously inpenetratable JN-167, another merchant shipping cypher.
A merchant-shipping cipher (see JN-152).
1942 Chicago Tribune incident 
In June 1942 the Chicago Tribune, run by isolationist Col. Robert R. McCormick, published an article that implied that the United States had broken the Japanese codes. This was a serious breach of national security. The government at first wanted to prosecute the Tribune under the Espionage Act of 1917. For various reasons, including the desire not to bring more attention to the article, the charges were dropped. 
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