The luxury project violated rules regarding the use and movement of freshwater sources, rock and sand, local authorities first alleged late last month and confirmed on Monday.
A spokesperson for Neymar declined to comment on the matter.
His residence is located in the town of Mangaratiba on the southern coast of Brazil's Rio de Janeiro state.
Mangaratiba's environmental body said in a statement on Monday that environmental infractions were made "in the construction of an artificial lake at the mansion."
Besides the fine, the case will be probed by the local attorney general's office, the state civil police and the environmental protection office, among other environmental control bodies.