"We are taking this proactive measure to slow down travel, and possibly help prevent the entry of the 2019-nCov," Jaime Morente, the commissioner of the Philippines' Bureau of Immigration, said in a statement, referring to the virus.
There is no order barring Chinese nationals from entering the Philippines, however, Morente added.
He did not say when the facility would be resumed. Chinese nationals can still apply for visas at any Philippine embassy or consulate at their places of residence.
Health authorities are monitoring more than 11 suspected cases of the new coronavirus, they said on Tuesday.
The "visa upon arrival" facility has been offered to Chinese nationals since 2017, in an effort to boost tourism. Those eligible included investors and businessmen, athletes, delegates to international conventions and tour groups.
Chinese tourists accounted for 22% of the 7.5 million visitors to the Philippines between January and November last year, making China the second top nation of origin for international travellers to the country.