Reston ebolavirus (Rebov) has only been seen in monkeys and humans previously and, unlike other types of Ebola, it is not known to cause illness in people.
Researchers say it is theoretically possible for the virus to mutate in pigs into a form that might sicken people.
The Philippines had tested 141 people, the researchers said, and six of them who either worked on pig farms or with swine products were found with antibodies to the Ebola-Reston virus, which means they might have been infected by pigs at some time.
However, they showed no signs of illness.
Rebov belongs to the family of filoviruses which target primates. These viruses cause viral haemorrhagic fevers, which result in bleeding and coagulation, and can lead to death.
In their study, the scientists examined blood and tissue samples taken from pigs suffering unusually severe respiratory infections in different parts of the Philippines and found they contained widely varying strains of the virus.
This suggests that the virus may have circulated widely in pigs even before it was first discovered in monkeys exported to the United States from the Philippines in 1989, the scientists said.
The discovery of Rebov in pigs in the Philippines is reported in Friday’s edition of the journal Science.