The Philippine government will slaughter 6,000 pigs on a farm near Manila where the Ebola-Reston virus has been found in the animals and its antibodies in humans, health officials said.
The cull is expected to start on a farm in Bulacan province where the non-lethal virus was found last year.
Eric Tayag, head of the National Epidemiology Centre, said the cull could take up to seven days to complete.
"It is better to depopulate this (farm) so there will be no fear it will spread," Tayag told reporters.
"The pigs will be humanely electrocuted, their remains burnt and then buried on the farm," he added.
According to the World Health Organisation, the strain infecting the pigs is not dangerous to humans, unlike the four deadly Ebola subtypes found in Africa.
The government earlier imposed a quarantine on two farms in Bulacan and Pangasinan provinces after samples found some pigs were carrying the Ebola-Reston strain.
The strain was first found in laboratory monkeys exported from the Philippines to the US in 1989.
So far, six farmworkers and butchers have been found with the antibodies.
Scientists are still trying to determine if the six caught the virus from pigs.
If such a link is proved it would be the first time humans have contracted the disease from pigs.