Duterte, has not been seen in public since Sunday and missed a scheduled appearance the following day.
Duterte, 72, has not been seen in public since Sunday and missed a scheduled appearance the following day at annual Independence Day celebrations in Manila, sparking speculation about the state of his health.
"He's just taking some time off to rejuvenate," presidential spokesman Ernesto Abella told reporters.
Abella said there was no date for when Duterte would resume his official duties, although he insisted the president was healthy.
"I'm saying that there's nothing to worry about in terms of sickness," he said.
"The president is well."
Pressed by journalists to state whether Duterte had visited a doctor this week, Abella said: "I'm not privy to those matters but I'm sure he's checked with his own experts."
Duterte was last seen in the southern city of Cagayan de Oro, visiting soldiers wounded in nearby fighting with Islamic State group-styled gunmen that is now on its fourth week.
Fifty-eight soldiers and police officers have died in the clashes in Marawi city, while at least 26 civilians have also been confirmed killed.
The militants remain holed up in pockets of Marawi alongside hundreds of trapped civilians being used as hostages or human shields.
Duterte imposed martial law over Marawi and the rest of the southern region of Mindanao, home to 20 million people, on the day the fighting erupted to head off what he said was an attempt by IS to carve out its own territory there.
Abella said Duterte was taking time off because of a punishing schedule since then, which included regular visits to military camps and hospitals to support troops.
"It has been really brutal, so it is important to allow him this kind of rest," Abella said.
Duterte had repeatedly denied during last year's presidential election campaign that he suffered from cancer.
However he said last December that he used to take fentanyl, a highly addictive synthetic opioid, to ease the pain of a spinal injury that he suffered in motorcycle accidents many year earlier.
Duterte said then his doctor made him stop using it on learning he was "abusing the drug" by using more than the prescribed amount.
Duterte's fentanyl comments attracted controversy as he has led a war on drugs in which thousands of addicts and users have been killed.
Under the constitution, the separately elected vice president shall act as president if the incumbent dies, is permanently disabled or removed from office.