More than 1,600 people have been affected and 100 hectares of crops destroyed in the cities of Baoshan, Lincang and Dali, Xinhua quoted the ministry as saying in a statement.
Five people have been reported missing in the floods.
The flash floods Monday struck Baoshan, a city in the western part of the province.
Relief material including quilts, blankets and tents have been sent to the area.
Heavy rain and flooding also hit Jiangsu, Jiangxi and Sichuan, the ministry added.
The flash floods come in the wake of Typhoon Matmo that struck eastern China provinces this week, while southern regions were dealing with the aftermath of Rammasun, the strongest typhoon to strike the country in four decades.