Health advocates have long-battled tobacco lobbyists and the eight firms now making cigarettes in the country.
Duterte signed an executive order this week for a nationwide smoking ban, prohibiting people from lighting up in all public places.
Ubial said Duterte signed the executive order on Tuesday, which sets strict guidelines on designated areas where smoking is prohibited or may be allowed, with breaches attracting a maximum penalty of four months in jail and a fine up to 5,000 pesos (100 USA dollars).
The authorities said the smoking ban also covers "vaping" or the use of electronic cigarettes.
There were similar smoking restrictions imposed in Davao City where he was mayor for more than two decades, the Telegraph reported.
Under the new law, tobacco can not be sold within 100 meters (330 feet) of schools, playgrounds or anywhere that children might gather.
Public conveyances, on the other hand, refers to "modes of transportation servicing the general population" like elevators, airplanes, ships, jeepneys, buses, taxi cabs, trains, light rail transits, and tricycles.
Duterte also ordered the creation of a smoke-free task force in all cities and municipalities to help carry out the provisions of the order.
In October a year ago, Duterte said the nationwide executive order is patterned after the smoking ban that he imposed when he was mayor of Davao City, his home city in the southern Philippines.More news: Russian president Putin warns world leaders to stop 'intimidating' N Korea
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Violators face a maximum penalty of four months in prison and a fine of $100.
The Department of Health (DOH) earlier hoped the EO would be issued by the end of October 2016, or before the full implementation of the Graphic Health Warnings Law.
Emer Rojas, a cancer survivor and the president of the anti-smoking group New Vois Association of the Philippines, said he hoped the new measure would significantly cut smoking in a country where it is common to see adults and children smoking on the street.
The EO says that the selling or distribution of tobacco products in a school, public playground, youth hostels and recreational facilities for minors or within 100 meters from any point of the perimeter of these places is also not allowed.
"This is a victory for us", said Maricar Limpin, executive director of Action on Smoking and Health Philippines.
Strict enforcement of a prohibition of tobacco sales to minors has been a challenge for the government.
Ubial said a number of tobacco control interventions, particularly tobaccos taxation, have led to a significant drop in current smokers from 17 million in 2009 to 15.9 million in 2015.