The 44-year-old Chinese national was one of two people to have the infection in the Philippines. Filipino health officials say the man arrived in Manila via Hong Kong on January 21 with a 38-year-old woman. She currently remains under strict observation but is no longer experiencing symptoms.
Both patients were from Wuhan in China’s Hubei province, the epicentre of the virus outbreak.
The Philippines’ Department of Health said the man developed severe pneumonia after being admitted to hospital.
His death is the first known case of a person dying from the virus outside of China.
Philippine health officials confirmed the first case of the new coronavirus in their country on January 30.
The health department’s announcement follows a move by the Philippine government to widen its travel ban amid the outbreak to include all foreigners coming from China.
Philippine President Rodrigo Duterte originally banned entry to travellers from China, Hong Kong, and Macau.
Early restrictions only included those who were travelling from Hubei province.
A temporary travel ban also stops Filipinos from visiting China and its special administrative regions including Hong Kong.
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Mr Duque said: “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.
“I would like to emphasise that this is an imported case with no evidence of local transmission.”
He added the man would be cremated to contain the virus.
Filipino authorities are starting to track down people who were on the same flight as the man and place them in isolation.
Officials are also contacting employees of hotels in which the infected patients stayed.
According to Hong Kong government statistics there are around 200,000 domestic workers from the Philippines working in Hong Kong as of 2018.
The Philippines has now offered voluntary repatriation of its citizens currently in China.
Filipino health officials emphasised there were no cases of human-to-human transmission in their country.
Many other safety precautions are now being enforced across the country.
Most shops in Manila have sold out of face masks and hand sanitisers.
The Catholic church said communion should be given into people’s hands rather than directly into their mouths and holy water should be regularly changed.