The Philippines recorded its highest number of daily infections in four weeks on Friday.
Indonesia's seven-day average of new cases reached its highest in more than two months on Sunday.
A surge of cases has also been reported near Myanmar's India border — raising concerns about a health system that has collapsed since the February 1 coup.
In the absence of vaccines, containment is the priority.
Vietnam crushed earlier waves — and the country of 98 million has still suffered fewer than 50 deaths — but new distancing measures started in its business hub Ho Chi Minh City on Monday.
In the north of the country, factories supplying global tech firms such as Apple and Samsung are operating below capacity because of outbreaks, industry sources said.
Thailand's largest agribusiness, Charoen Pokphand Foods, closed a poultry factory for five days after workers tested positive for Covid-19. Thousands of more cases have been found at factories, construction sites, and prisons.
As Malaysia ordered a "total lockdown" from today to stem the spread, officials said some factories could keep operating at reduced capacity.
Health officials are also watching closely for any resurgence in Indonesia and the Philippines, the region's two most populous countries, which were both hit hard by the pandemic last year.
Slow vaccination rates
Malaysia has tried to step up its vaccination campaign, but fewer than six percent of people have received at least one dose of a vaccine — barely half the proportion in India.
Some South-East Asian countries had placed less emphasis on vaccine procurement than Western countries or simply could not afford them and now have limited access.
"With a smaller segment of the population that is protected from vaccination, the vast majority of the population remains susceptible," said Teo Yik Ying, dean of the Saw Swee Hock School of Public Health at the National University of Singapore.
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