Cameroon-born N'Dam was sent to the canvas in the fourth round after being caught by a powerful right cross and seemed to be in survival mode for the rest of the contest but two of the three judges gave the win to the 33-year-old.
"After judging the bout, my scorecard is 117-110 for Murata," said WBA president Gilberto Jesús Mendoza in a statement.
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"First of all, let me apologise to Ryota Murata, Teiken Promotions and all Japanese boxing fans. There are no words to repair the damage... I will demand the Championships Committee to order a direct rematch.
"I am disappointed with the controversy. My goal is to have clear decisions and prove transparency to all boxing fans."
The defeat was 2012 London Olympics gold medallist Murata's first as a professional after 12 straight wins, while N'Dam improved his record to 36-2.
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