Nine workers were using heavy machinery to remove sea water from the open-pit mine when a wall collapsed and buried the miners, Governor Rhodora Cadiao said.
Heavy rains had also reportedly drenched the area, she added.
"Nine people were buried and presumed dead. We recovered three bodies and we're looking for six more," Cadiao told radio DZBB.
Mining operations were suspended following the incident and investigation has been launched.
"Precautionary measures should have been in place," the governor said. "This will undergo (an) investigation. I hope there is no negligence on the part of the contractor."
The open-pit mine is on an island around four hours by boat from the central island of Antique, a fishing province in the Visayas islands, and one hour by plane from the capital Manila.