The environmental protection prosecutor's office had already slapped a $500,000 fine on Dragon Mart last month because it lacked proper environmental impact authorizations.
This time, the agency issued a fine of $208,000 and ordered the Chinese-funded project to pay almost $900,000 to repair the damage.
The $180 million project, financed by the Chinamex company, has been criticized by environmentalists because 418 hectares (1,032 acres) out of the total 557 on which the mall is to be built is located on land designated as a nature reserve.
The project stalled initially after authorities refused to issue a construction permit but got going after several rounds of legal appeals.
The mall, which would be the second largest Chinese retail complex in the world outside China, is scheduled to be inaugurated in November.