The Ebola-Reston strain, however, was believed to have affected only domestic livestock and had not jumped to humans, said Agriculture Secretary Arthur Yap.
Pigs on at least three farms in the provinces of Bulacan, Pangasinan and Nueva Ecija have been quarantined for further tests.
This was the first case of Ebola-Reston found in pigs rather than monkeys, and the government was closely working with the World Health Organisation and the World Organisation of Animal Health in carrying out further tests, Yap said.
"This is the first time Ebola has been detected in pigs, but this is not a human health issue, but an animal health problem," Yap told local radio.
"There is no evidence that this could jump to humans," he said, adding that Ebola-Reston was different from African strains that cause deadly haemorraghic fever, which has led to hundreds of human deaths in Africa.
Yap said he had issued a temporary ban on exports of Philippine pork until the virus was completely eradicated from livestock.
He said the farms were being closely monitored. Farm hands and butchers had been tested, but results had so far come back negative.
Other pigs on the farm were not infected, while old stocks of meat had been burned as a precaution, he said.
Ebola-Reston was first discovered in 1989 in monkeys sent from the Philippines to a research facility in the US city of Reston, Virginia.
According to the WHO's website, investigations traced the source of the outbreak to an export facility near Manila "but the mode of contamination of the facility was not determined".
Several monkeys died, and at least four people were infected, although none of them suffered clinical illness, the WHO said.
Similar outbreaks in monkey populations were found in 1992 and 1996 in the southern Philippines.
A source at the WHO said this is the first time the Ebola-Reston virus had been found in pigs.
While the four strains of the Ebola virus found in the Democratic Republic of the Congo, Sudan, Ivory Coast and recently Uganda are known to be deadly to humans, the Ebola-Reston virus was not, the WHO said.
Jane Bacayo, executive director of the National Meat Inspection Service, said the Ebola-Reston virus was accidentally discovered when they sent samples to US authorities to find a cure for another disease killing local pigs.
They were surprised to find out that an alert was raised after some samples tested positive for the Ebola-Reston strain.
He said quarantine checkpoints had been erected on major highways to prevent transport of pigs from the affected areas.
"We are trying our best (to prevent) the virus from spreading in other farms in the country, or infect humans," Bacayo said, adding that the hog industry's export potential would be further damaged unless the virus was purged.
The head of the government's National Epidemiology Centre, Eric Tayag, said the public should not panic since the virus found locally was not pathogenic to humans.
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