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 an investigation has been launched.
Five people were killed in a similar incident at the mine in 2013.
"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."
Semirara Mining and Power Corp., which owns the mine, said it was investigating in coordination with the government.
"Management has condoled with the families of the victims and is giving them full support," it said in a statement.
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.
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