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," said Cadiao.
Mining operations were suspended following the incident and investigation has been launched.
A similar accident in 2013 in Semirara in Antique, about 350 kilometers (215 miles) south of Manila, killed at least 5 workers.
Coal makes up for about a third of energy supply in the Philippines.
The accident site 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.
OneIndia News (With agency inputs)