Police said torrential monsoon rain inundated the mine in Jhampir, 120 kilometres (75 miles) east of Karachi.
Poverty and the weak implementation of labour laws see millions of children exploited in often hazardous work environments in Pakistan.
"The mine is about 350 feet (110 metres) deep and we are trying to recover the body of the boy," Zahid Sheikh, a local police officer told AFP.
The chief minister of southern Sindh province, where the mine is located, has ordered an enquiry, officials said.
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