Vandals broke into Yerucham's the Tiferet Yisrael synagogue and the B'levav Shalem yeshiva on Thursday.
Yerucham is a town of nearly 10,000 Jews, located 36.5 kilometres (22.7 miles) south of Be'er Sheva.
The vandals destroyed the Holy Ark, desecrated the Torah scrolls, stole the scroll's cover, and threw the parchments on the side of the road, into mud and water. The damage is estimated to be in the hundreds of thousands of shekels.
In a break-in at Tiferet Yisrael earlier this month, charity boxes were forced open and the vandals destroyed the building, damaging books and furniture. Similar events have occurred at the B'levav Shalem yeshiva. Complaints were submitted to Israel Police, but according to residents, nothing has been done.
Rabbi Yitzhak Shalev, Yerucham's rabbi, said: "The entire city of Yerucham is in upheaval. There's no one who heard about the destruction of the Torah scrolls and was left unaffected. The sorrow and shock belong to our city's entire community, regardless of affiliation. No one believes that we've witnessed something like this."
"We all want and need to adhere to all of the authorities' health guidelines, but it is unthinkable that specifically because of the current crisis, the People of Israel's holy things - the Torah scrolls and synagogues - will be damaged. We need to know that a Torah scroll in any place in the world is not the Torah scroll of the Jones family or a given synagogue. It's everyone's Torah scroll, and debasing the honor of Torah scroll and desecrating it, is debasing the honor of all of Israel.
"It's unthinkable that in our country, the only country of Jews in the entire world, Torah scrolls will be desecrating in such a horrific and embarrassing way.
"We demand quick and efficient intervention from all the authorities in this issue. We all have an obligation to protest, in honor of what is holy, and the best way to do that right now is to participate in the cost of fixing the scrolls. The vandals tried to minimize what was holy and to harm it, because they wanted money or because of some other desire, and in contradiction to their opinion, we will add in holiness. We will show that desecration of a Torah scroll's honor touches all of us."