Eighty medical associations representing tens of thousands of doctors signed the open letter, a day after the country posted a record single-day count of more than 4,000 new infections, pushing the total past 93,000.
"Healthcare workers are united in sounding off a distress signal to the nation -- our healthcare system has been overwhelmed," the letter said.
"We are waging a losing battle against COVID-19, and we need to draw up a consolidated, definitive plan of action."
An increasing number of health workers have fallen ill or quit their jobs, while some packed hospitals are now refusing to admit new patients, it added.
The government has blamed poor compliance with health protocols for the sharp increase in infections.
The country imposed one of the harshest lockdowns in the world in mid-March, that kept people at home except to buy food and seek health treatment.
But the government recently loosened the restrictions to allow people to return to work after predictions that the Philippine economy will fall into recession, with millions of jobs already lost.
In the open letter, doctors urged Duterte to put the capital Manila and surrounding provinces back under "enhanced community quarantine" until August 15 to give the country time to "refine our pandemic control strategies".
In response, Duterte's spokesman Harry Roque said the government was balancing the health and economy of the nation.
"The strict lockdown in Metro Manila has served its purpose, and we need to intensify other strategies," he added.
Health department officials earlier this week acknowledged hospital bed availability was drying up and the government has had limited success in hiring new doctors, nurses and other health care workers.
The letter said contact tracing was "failing miserably" and public transport and workplace settings were often unsafe.
Lei Alfonso, an official of the Philippine Society of Public Health Physicians, told a news conference on Saturday that the developments "will push us to the brink to become the next New York City, where Covid-19 patients die at home or (on) stretchers".
President Duterte on Thursday called on Filipinos to keep faith in his ability to swiftly procure a vaccine to be produced by China, a key supporter of his rule.