Eleven captive Philippine macaques have died after contracting the bat-borne Ebola Reston virus while nine others are under treatment, they said.
"All exports are suspended while we investigate this incident," Simeon Amurao, assistant director of the Bureau of Animal Industry, told AFP.
The Philippines is among the world's major exporters of laboratory monkeys and has so far shipped close to 300 monkeys to Japan this year, and 600 last year, Amurao added.
"This kind of Ebola is the least harmful in terms of human affectation. This is limited to monkeys," Health Secretary Janette Garin told reporters.
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She said 62 workers in two monkey-breeding facilities all tested negative for infection in August following the deaths of 10 macaques that had exhibited Ebola symptoms.
The 10 fatalities were traced to two other undisclosed breeding centres where another 10 tested positive for the virus, one of which died, she said.
It was the first case of Ebola Reston among Philippine macaques since 1997, according to the agriculture department.
In 2009, 6,000 pigs at a farm in Manila's northern suburbs were slaughtered after they tested positive for Ebola Reston.