New York schools are closing a lot. This is about to change.

Mayor Bill de Blasio will change a rule that has, for months, created a paradox in New York City’s school reopening plan: classrooms that were reopened to students often close again because school buildings had to temporarily close whenever two cases of unrelated viruses have been detected.

The mayor announced Monday that he would change the rule, but did not explain how. He said the new rules would be outlined in the next few days, but he did not commit to making changes this week.

The closure rule has been extremely frustrating for many parents, who say that every day brings uncertainty about whether their children will be able to go to school the next morning. Many schools have closed several times and sometimes opened just a few days before the next closure. The rule was also extremely disturbing for educators, who were forced to switch between face-to-face and online learning just a few hours in advance.

The controversy over the closure rule highlighted the enormous difficulties and compensations inherent in the reopening of schools during the pandemic. Mayors and educational leaders across the country have been struggling to find ways to return students to classrooms while experiencing security protocols in real time.

Closures have accelerated in the past few weeks and months, as elementary and high school students have returned to their buildings after months of totally remote learning. The vast majority of students in New York City – about 700,000 out of 1 million – chose to learn remotely full-time, meaning that the closure rule did not affect most families.

But the city is giving all families the opportunity to switch from distance learning to classroom teaching for the rest of the school year, so that number may change. Some students will receive full-time instruction, while others will go on some days of the week and learn at home the rest of the time, based on individual school ability. Families have until the end of Friday to change.

In recent weeks, some epidemiologists and medical experts have told ProPublica and the educational news website Chalkbeat that the New York two-case rule was arbitrary and led to unnecessary closings, and asked the mayor to adjust it.

“The way to beat Covid is not by closing schools excessively, but by suppressing broadcasting inside and outside schools,” said Dr. Dave A. Chokshi, city health commissioner, during a news conference on Monday.

City schools have had very low virus transmission in classrooms since they started reopening last fall. Michael Mulgrew, president of the United Federation of Teachers, vehemently opposed any change to the rule for months, arguing that city schools were safe only because of strict security measures, including the two-case limit.

“We can’t just say why they are an inconvenience that we don’t want them,” Mulgrew said of the guidelines during a radio interview last month.

The closure rule was agreed last summer, during a period of intense turmoil between the city and the union, at a time when it was not clear whether de Blasio would be able to reopen schools. The city and the union finally agreed to a series of safety rules that paved the way for New York to become America’s first major school district to reopen schools for all grades.

Several of these rules have changed in the past eight months. The mayor said during the summer, when the city’s average test positivity rate was hovering below 1 percent, that the entire school system would close if the positivity rate reached 3 percent, which happened in November. He closed the school system for several weeks, but came under strong pressure from parents and experts to set a different limit.

When Mr. de Blasio reopened schools for young children and some students with disabilities in December, he said there would no longer be a limit of positivity across the city to close the school system.

The city is also on the verge of partially changing a rule it established over the summer, which required two meters of distance between students in classrooms. Last month, the Centers for Disease Control and Prevention said that districts should consider reducing the distance to one meter, a standard that Mr. de Blasio said the city would adopt in elementary classrooms later this month.

This change angered the teachers’ union, which had a significant influence on the school’s reopening process in New York. Although relations between the city and the union have been icy for months, the mayor tried to maintain peace with Mulgrew.

For example, when the city reopened elementary schools last year, despite the increase in cases of viruses across the city, de Blasio announced an increase in randomized tests on school buildings, a consistent union priority that experts have supported.

But the city and the union have been struggling to agree on the two-case rule. For weeks, de Blasio said a revision of the rule was imminent, but behind the scenes, negotiations between the two sides were stalled. The city and the union have not yet reached an agreement on what the new closure limit should be.

While the mayor has the power to change the rule unilaterally, the city has tried to prevent the union from leaving with only a few months to go until the end of the school year. UFT raised many questions with the city about the reopening plan last summer, but is more willing to reopen schools than some other teacher unions in major cities, including Chicago and Los Angeles.

The fact that all grades in the school system are open means that the union has less influence now than at any time during the school’s reopening process. But the union still has a huge influence on the course of the next school year.

De Blasio said he expects full-time face-to-face classes until September, although there is likely to be a remote option for some families in the fall. This goal will depend, in part, on union cooperation and support, and teachers will undoubtedly play a crucial role in reaching reluctant families and encouraging them to return to the classroom.