Mutko pointed to Irish lightweight Katie Taylor's 10-8 win over Russia's Sofya Ochigava in the women's boxing final on Thursday.
"How can you give such scores? You'd have to be blind," Mutko was quoted by RIA Novosti news agency as saying.
The head of Russia's Olympic Committee, Alexander Zhukov, said the judges may have been swayed by the enthusiastic cheering from the Irish fans. Mutko, however, was less forgiving and suggested that the judges have favoured the host nation's athletes.
"We see that a happy ending is being prepared in boxing," he said.
British boxers are competing in the welterweight and super heavy weight finals on Sunday.