Cameroon-born N'Dam went to the canvas in the fourth round after being hit by Murata's powerful right cross and seemed to be in survival mode for the rest of the fight.
Two of the three judges, however, gave the victory to 33-year-old N'Dam, who now has a 36-2-0 career record.
Murata, the 2012 Olympic middleweight champion who was facing his first big test at the age of 31, suffered his first defeat in 13 fights.
Kazakh Gennady Golovkin is the category's unified champion.
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(Reporting by Julien Pretot in Paris; Editing by Ken Ferris)
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