The Philippine health ministry said the B.1.1.7 variant had spread among 12 people in Bontoc, a mountainous northern province, with 17 such cases in the country.
Its first case of the British variant was found in a Filipino who had travelled from the United Arab Emirates.
Citing the British variant, Duterte said he had scrapped a plan to allow children ages 10 to 14 in low-risk areas to go outside the home starting February 1.
The Philippines, which has imposed some of the world's toughest coronavirus restrictions, including internal travel bans, has since March last year officially prohibited minors from leaving the home.
“I am afraid because this new strain strikes the young children,” Duterte said late Monday. “They can glue their attention on TV the whole day.”
The government had hoped easing restrictions on children might boost economic activity, after a year when growth is expected to have contracted 8.5%-9.5%.
With nearly 515,000 coronavirus cases and more than 10,200 deaths, the Philippines is among the worst affected countries in Asia.