The matter was reported by a match delegate after the anthem was jeered by home fans prior to City’s Champions League victory over Sevilla on Wednesday.
City have been charged under article 16 of Uefa’s disciplinary regulations which lists “the disruption of national or competition anthems” as “inappropriate behaviour”.
A Uefa spokesperson said: “Uefa has opened disciplinary proceedings for the disruption of the competition anthem at last night’s match. The disciplinary body will deal with this case on November 19.”
City are thought to be bemused by the development and could consider making representations to defend the rights of supporters to freedom of expression and peaceful protest.
City fans have regularly booed the Champions League anthem in protest at the financial fair play punishment meted out to the club by Uefa in 2014 when
City were fined £49 million.
City manager Manuel Pellegrini this week refused to criticise supporters over the booing.