An immediate cull was ordered for all chicken, ducks and quail within a kilometre (0.6 miles) of the infected poultry in San Luis town, north of Manila, said Agriculture Secretary Emmanuel Pinol.
The health department was meanwhile monitoring the health of farm workers exposed to the infected birds, he added.
"So far we do not have any reported animal to human transmissions," Pinol told a news conference.
Pinol said the infected birds tested positive for avian influenza Type A, sub-type H5.
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Philippine officials have not yet said which H5 subtype the infected birds carried.
"The transmission risk is low, but the mortality is high. It is a concern," said Carlos, especially for infants as well as people suffering from other ailments.
The World Health Organisation has monitored 453 human deaths from 859 cases of avian influenza since 2000, with Asia accounting for 41 per cent of all cases.
The Philippines had not previously reported any human cases, according to WHO data.
The six infected Philippine farms only sold their products to local consumers and none had been exported, Pinol said.
However, the outbreak began in April and the farm owners had neglected to report it to the authorities immediately, he added.
To prevent the potential spread of avian flu, the government has banned the transport of all poultry products from within seven kilometres of the infected farms, Pinol said.
He said the authorities suspect the virus could have been spread by migratory birds or from smuggled poultry products.