Residents must wear masks indoors and outdoors in the Binjamin region, south of Haifa, and in Modina-Macabima-Reut.
The decision came a few days after Israel lifted the requirement to wear masks, given the declining number of infections.
However, at the school in Binjamin, 45 students have now been confirmed to be infected with the coronavirus, and in Modina, between Tel Aviv and Jerusalem, about ten.
Outbreaks in schools are linked to the return of residents from foreign trips, as well as infection with the most contagious, delta variant of the virus, the media reports.
Two weeks ago, Israel started vaccinating 12- to 15-year-olds against Covid-19.
The country, with a population of nine million, launched a vaccination campaign in December. Nearly 5.5 million people have received the first vaccine, but more than 5.1 million have been fully vaccinated.
The number of severe cases has fallen sharply in recent months. There are currently 22 such cases, but there were still about 1,200 in January.