MANILA, Philippines — Millions of students throughout the Philippines headed to school Monday as in-person classes began to fully restart for the first time in more than two years, ending one of the world’s longest pandemic-related shutdowns in a school system already plagued by severe underinvestment.

“We could no longer afford to delay the education of young Filipinos,” said Vice President Sara Duterte, who is also the education secretary, as she toured schools in the town of Dinalupihan, about 40 miles northwest of Manila.

Even before the pandemic, the Philippines had among the world’s largest education gaps, with more than 90% of students unable to read and comprehend simple texts by age 10, according to the World Bank.

Schools in the Philippines have long suffered from shortages of classrooms and teachers, whose pay is low, leaving the vast numbers of poor children who cannot afford private schools and rely on the public system with inadequate teaching.

Now, after losing more than two years of in-person instruction, schools face the monumental challenge of educating many students who have fallen even further behind. Although the Philippines offered online instruction during the pandemic, many students lacked access to computers or internet connections, and overburdened parents often found it hard to keep tabs on their children’s remote learning.

In some cases, students’ already tenuous connection to school may have been severed entirely after so long away.

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“As we welcome children back into the classrooms today, let’s remember that this is the first of many steps in our learning recovery journey,” said Oyunsaikhan Dendevnorov, the UNICEF representative in the Philippines.

In many countries, as the shortcomings of online learning became increasingly well documented —especially for more disadvantaged students — governments elected to send children back to classrooms even as the coronavirus continued to circulate widely.

A World Bank report that examined 35 studies from 20 countries concluded that the longer schools remained closed, the more ground students lost, with potentially far-reaching consequences. “The inequality in learning between advantaged and disadvantaged groups is likely to grow,” the report said, “posing a significant challenge to ending extreme poverty and promoting shared prosperity.”

Many children simply dropped out. In Uganda, for example, 1 in 10 students did not report back for classes when they resumed in January after what was one of the world’s longest shutdowns, according to UNICEF.

In the Philippines, government officials and parents were hesitant to reopen classrooms, fearing that schoolchildren could bring the virus back to homes crowded with multiple generations of family members and overtax an already creaky health care system.

Starting in late 2021, the government began to experiment with conducting in-person classes in about 300 schools, but has now begun expanding it to cover all primary and secondary schools. Currently only some schools are in-person all five weekdays; by November, all of the country’s roughly 47,000 schools will be.

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Duterte said the number of those enrolled in the country has hit nearly 28 million children, both in the public and private schools.

Maria Rogas, a mother of three in suburban Bacoor City, south of Manila, said she had mixed feelings about sending her children back to school.

On the one hand, she welcomes the return to normalcy, but on the other, “COVID remains a scary problem.”

Data from the Department of Health shows that only roughly 27% of children ages 5 to 11, and about 76% of those between 12 and 17, have been fully vaccinated.

To make it easier for children to get their shots, local health officials were encouraged to set up satellite vaccination sites at schools. However, this was not mandated by the government at the national level. Vaccinations remain purely voluntary, and widespread hesitancy is a problem.

President Ferdinand Marcos Jr., who last month ruled out more economically crippling lockdowns amid the pandemic, on Monday stressed that learning was more effective if classes were done physically in schools, but also called on the public to observe proper health protocols.

Rogas, 43, said her children had been vaccinated, but she still worried. “You never know about this virus, which mutates every so often,” she said.

For now, she said, they were just happy to return to school. “For two years, they only saw their friends and classmates on small screens, so they are excited to interact with them.”