Rabindra Abeyasinghe, the WHO representative to the Philippines, urged people to remain calm: "This is the first reported death outside China. However, we need to take into mind that this is not a locally acquired case. This patient came from the epicentre of this outbreak."
According to local news outlet Rappler, Health Secretary Francisco Duque III said the patient was "stable and showed signs of improvement", but his condition deteriorated over the last 24 hours.
"We are currently working with the Chinese embassy to ensure the dignified management of the remains according to national and international standards to contain the disease," Mr Duque said, adding that the man would be cremated.
The Department of Health was now trying to track down people who were on the same flight as the man so that they can be quarantined, he said, as well as any other people the man and woman may have come into contact with, such as hotel staff.
The man's death was confirmed shortly after the Philippines announced it would also immediately halt the arrivals of any foreign travellers from China.
It had previously restricted only those from Hubei, which is at the epicentre of the outbreak.
Countries around the world have closed their borders to people coming from China, as officials work to control the rapid spread of the virus.
The US and Australia have said they will deny entry to all foreign visitors who had recently been to China, where the 2019-nCov strain of the coronavirus first emerged in December.
Other countries including New Zealand, Russia, Japan, Pakistan and Italy have also announced similar travel restrictions.