The facility's 25 workers have been tested for possible infection but all have been found negative for the Ebola Reston variety, said Health Secretary Janette Garin.
She said the virus was detected last week after the monkeys were observed to be suffering from measles, which could have lowered their resistance to Ebola.
Garin provided scant details, and did not identify the facility, the location or whether the monkeys were being also bred for export to foreign laboratories. Meanwhile, the monkeys will continue to be observed, she said.
"There are many types of Ebola," she said. "This Ebola is the kindest to humans."
A deadly Ebola strain killed nearly 8 000 people over the past two years in West Africa, causing global concern over the spread of the virus.
Garin said that authorities at the World Health Organisation, which has a regional office based in Manila, have been informed.
It was the latest reported Ebola infection in mammals in the Philippines since 2009, when pigs tested positive for the virus at a hog farm in Bulacan province north of the Philippine capital. About 6 000 pigs were then culled to prevent the spread of the virus.
Health officials also said that six farm and slaughterhouse workers had developed antibodies to the virus after coming in contact with infected pigs, but they did not suffer from any serious illness over the previous 12 months.
In 1996, monkeys that originated from the Philippines were found with Ebola Reston at a laboratory in Alice, Texas. About 600 monkeys at the Philippine breeding facility were killed to control the spread of the virus before the facility was shut down.
The first reported Ebola-infected monkeys from the Philippines were found at a research laboratory in Reston, Virginia, where dozens of them died in 1989.
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