The move is a possible sign of a shakeup in roles ahead of a crucial Communist Party congress later this year.
The South China Morning Post said Monday that Sun Zhengcai is being investigated by the ruling Communist Party's anti-graft arm.
The Chongqing government said on its website Saturday that Sun Zhengcai was being replaced as head of the city's Communist Party committee by Chen Min-er.
Both Sun and Chen sit on the party's 25-member Politburo and are considered candidates for promotion to the body's Standing Committee, the apex of political power in China.
The Chongqing announcement gave no details on the move.