The fire blackened the entrance mat and melted two plastic plants.
Members of the community, which numbers about 40 families, said that the incident comes just two weeks after a sign was placed on the façade of the synagogue identifying it with the Masorti movement.
But police said that fire was set by bored teenagers and that there was no suspicion that the attack was religiously motivated.
The building, the community's first permanent house of prayer, was built over a year ago with help from the Housing and Construction Ministry and the Modi'in Municipality.
"The damage was minimal but the shock is great," said Naomi Dar, chairperson of Yedid Nefesh."The attack was definitely aimed against us," added Dar who admitted that except for a few isolated incidents, Masorti Jews always felt welcome and comfortable in Modi'in.
But Supt. Yoram Barina, commander of the Modi'in police station, said that the arson incident was the work of "bored youths on summer vacation" and rejected the possibility that the fire was started by individuals ideological opposed to the Masorti movement.
"This was just a prank by a bunch of kids who played around with fire," said Barina.
Modi'in Reut Spokesman Elad Shimonovich said that an investigation by the Modi'in security department and Modi'in Police revealed that the incident was an act of vandalism by teenagers, and not an attempt to firebomb a synagogue motivated by ideology or religious conviction.
"This is a prefab building that from the outside does not look like a synagogue and therefore the youths were not conscious of their actions," said Shimonovich.
Chief Rabbi of Modi'in David Lau, who is Orthodox, said in response to the incident that "burning synagogues was never the way of the Torah."
Dar said that about three years ago a group of haredi youths disrupted prayers and scared children of the community during Pessah services. Police detained some of the youths, who were ordered to apologize to the community.
Dar said that in another incident, a former municipality representative from Shas publicly denounced the Masorti movement during a discussion on land allocation for the Yedid Nefesh synagogue.
"But in general, the municipality and citizens here are very accepting of us. We never receive bad feelings from anyone," he said.
Attorney Yizhar Hess, executive director and CEO of the Masorti Movement in Israel, said in response, "We are surprised and shocked by the attempt to damage the synagogue because Modi'in and the municipality is pluralistic, open and accepting and open to all three streams of Judaism.
"It is difficult to tell whether this was a religiously motivated attack or pointless vandalism but we hope that this is a one-time incident that will not repeat itself," he said.
This was not the first arson attack on a Masorti synagogue. On a Saturday night in June 2000, arsonists threw Molotov cocktails into one in the Jerusalem neighborhood of Ramot, setting fire to the building's interior and causing thousands of dollars of damage.
The firebombing had been preceded by an attempt a few weeks before to burn the front door of the same synagogue.
Rabbi Menachem Creditor
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