Additional cases have also been identified in some northern provinces, the Department of Agriculture said.
The world's 10th-largest pork consumer and seventh-biggest pork importer reported its first-ever African swine fever outbreaks in September 2019 in some backyard farms near the capital Manila on the northern island of Luzon.
But a week ago, the agricultural department said samples from pigs in the southern province of Davao Occidental had tested positive for the highly contagious disease.
On Sunday, the department said 407 pigs had been culled in two villages, with a swine population of 2,398, in Davao City on the southern island of Mindanao. The island had a swine herd of around 3.7 million as of 1 January, government data shows, or 29 percent of the country's total.
Agriculture Secretary William Dar had consulted Mindanao government officials and hog industry leaders to effectively manage and contain the outbreak, the department said in a statement.
The Davao Occidental outbreak may have been triggered by food waste from pork products from Indonesia, or food brought home by residents from disease-hit areas in Luzon, the agricultural department said.
More cases have recently been reported in some Luzon provinces, including Pangasinan, which was among the areas hit last year, and in Kalinga and Benguet provinces.
Dar has said pork smuggled from China, where millions of pigs have been culled because of the disease, could be behind the first outbreak in the Philippines.