It was the first reported case of African swine fever infections in Davao Occidental province and elsewhere in Mindanao, the southern island of the Southeast Asian nation.
Agriculture Secretary William Dar has ordered regional department officials to restrict animal movement in that part of the archipelago, the department said in a statement.
The Philippines, also the world's seventh-biggest pork importer, reported its first African swine fever outbreak in September 2019, in some backyard farms near the country's capital, Manila.
The disease quickly spread to other parts of the main island of Luzon, including Manila, prompting some central and southern provinces to ban pork and pork-based products from disease-hit areas.
Dar has said pork smuggled from China, where millions of pigs were culled because of the disease, could be behind the outbreak in the Philippines.
Although the blood samples from pigs in Davao Occidental had already tested positive for African swine fever, further tests were to be undertaken by the department's Bureau of Animal Industry for confirmation.
The department said the initial tests covered blood samples from more than a dozen villages in the province.
The provincial government has already imposed a "complete, but temporary, lock down," prohibiting the transport of pigs and pork products from and into Davao Occidental, it said.
"Backyard pig farmers in the area practice group rearing of hogs, from different owners, most (of them without) proper housing provisions nor biosecurity practices," the department said.
There was also no regular vaccination, vitamin supplementation and deworming of pigs in the province, and household butchering is common, especially with animals exhibiting weakness or disease, it said.
Around a thousand pigs in Davao Occidental have been culled amid the outbreak, according to local media reports, citing information from the provincial government.
Philippine agricultural output grew at an annual pace of 0.4% in the last quarter of 2019, slower than the 2.9% gain in the September quarter, as hogs production contracted.Though not harmful to humans, the disease is deadly to pigs, with no vaccine available.