Duterte approved a resolution allowing a raft of measures including bans on mass gatherings, a month of school closures and community quarantining, and threatened to jail local officials who defied government orders.
The firebrand leader, who underwent a test himself on Thursday due to possible exposure, said the measures would include banning foreigners traveling from countries with domestic transmissions from entering the Philippines.
It follows confirmation on Saturday of the Philippines' first domestic transmission of the virus, and a subsequent rise in cases daily to 52, among those five deaths, resulting in the Manila lockdown.
"We do not want to use that (term). But it is a lockdown," Duterte said in a televised announcement.
"There is no struggle of power here. It is a matter of defending and protecting you from COVID-19."
The curbs on travel and scope for mass quarantining would be among the strictest domestic coronavirus restrictions outside China and Italy, which have combined more than 90,000 confirmed cases.
Duterte last week attended the same event as an official who later tested positive for the coronavirus, and would know his result on Saturday. Six cabinet ministers, 16 lawmakers, six Manila mayors and the central bank governor were undergoing self-quarantine as a precaution.
Despite having relatively few confirmed infections, health authorities are keen to halt the spread of the virus, having last year dealt with major outbreaks of dengue and measles, and the first cases of polio in two decades.
The biggest concern is Manila, an urban sprawl of 16 cities fused together, known for its overcrowded slums, limited open spaces and horrendous traffic congestion.
Its population is officially nearly 13 million, but the real number is believed to be far greater due to unchecked migration and millions of informal settlers.
The resolution advises quarantining urban communities where there are confirmed cases in two separate households, and extending that to municipalities and cities where there are outbreaks in different districts.
Duterte said it was possible the measures "could create public disturbances or disorder," but hoped people would see sense."It is a serious one, it is true," he said. "Do not kill yourself with worry because government is doing everything possible to make it at least controllable."