The Philippines has indefinitely suspended the operations of the country's largest gold mine after a waste spillage near a major river, officials said Monday.

Philex Mining's Padcal facility will remain closed until a government investigation determines the extent of the spill and why it happened, said Leo Jasareno, head of the government's Mines and Geosciences Board.

"It is currently suspended indefinitely," he told AFP, adding the inquiry would last at least a week and examine whether any toxic substances had leaked at the mine, near the northern mountain resort of Baguio.

There was a spill at the mine's tailings pond last week after the Philippines was battered by heavy rains from Typhoon Saola, raising fears that toxic substances could enter major waterways.

Government scientists later concluded the slime and silt did not reach the Agno river and the nearby San Roque dam, one of the country's largest.

Philex Mining vice-president Mike Toledo said the company stopped operations at the mine when it discovered the leak.

"We will not operate until such time that we are certain (the tailings pond) is okay," he said in a statement.

Philex had previously insisted the spillage consisted only of water and sediment, which were "non-toxic and biodegradable".

The accident came amid intense public debate about the mining industry in the Philippines, which is believed to have some of the biggest mineral reserves in the world.

However the wealth remains largely untapped, partly because of a strong anti-mining movement, while poor infrastructure and security concerns have also kept investors away.