Thirteen members of a Hasidic Jewish community were arraigned on Wednesday on charges stemming from a January incident in which a wall inside a famous Brooklyn synagogue was damaged by young men wielding a hammer and crowbar — setting off a melee that was captured on video.

The 13 people, all young men, pleaded not guilty in State Supreme Court in Brooklyn to charges that ranged from criminal mischief to obstructing governmental administration. Another four defendants were absent because they were in Israel, according to their lawyer, Levi Huebner.

Justice Adam Perlmutter ordered the defendants, many of whom are from Israel, to turn over their passports. He denied prosecutors’ request to ban the young men from the synagogue, on Eastern Parkway in Crown Heights, Brooklyn, which is where they both worship and study.

The synagogue is a part of a complex of buildings that are centered by a gothic revival structure at 770 Eastern Parkway and is the global headquarters of the Chabad-Lubavitch movement. Referred to as 770, it is one of the most significant religious sites in New York.

According to Mr. Huebner, most of the defendants came to New York from Israel to study the Torah and the teachings of Rabbi Menachem Mendel Schneerson, known as the Rebbe.

The Rebbe, who died in 1994, is considered to be the messiah by many in the Lubavitch movement, and during his lifetime he called for the expansion of the synagogue, which is packed sardine-like every day with worshipers from around the world. The squeeze on the Sabbath and Jewish holidays is even more extreme.

In January, after news reports revealed that a space adjacent to the synagogue had been secretly excavated, the building owners called for cement trucks to fill the space. Before they could, some students broke through the wall between the dug-out space and the synagogue, the police said. They appeared in video footage being cheered by fellow students as they were arrested.

“They did it to expand 770 and make it bigger,” a man who gave his name as Zalmy Grossman said in January. “They have come to fulfill the rebbe’s wishes.”

None of the young men charged in the January incident are accused of excavating the passage outside the sanctuary.

City inspectors and the media referred to the excavated space as a “tunnel,” a characterization which many in the Lubavitch movement say maligns and casts unspoken suspicions upon the insular community.

The city’s Buildings Department closed down parts of 770 to investigate the damage and issued two citations for the excavation, which was conducted without proper permits. By the end of the week, the excavated space had been filled with cement, and city inspectors allowed the synagogue to open again.

At the hearing on Wednesday, the indicted men wore traditional Lubavitch dress of dark suits and skullcaps, placing their large black fedoras on their laps as they sat in the courtroom. Most ranged in age from 18 to 21, and few spoke English fluently.

Mendel Gerlitzky, who was arraigned on charges of criminal mischief and reckless endangerment, was raised in Brooklyn and prays at 770 three times a day. While many of his fellow defendants declined to comment, Mr. Gerlitzky did not hesitate to draw attention. On the lapel of his black suit, he wore a pin in the shape of a shovel. It featured a tiny etching of the synagogue and the words “expand 770.”

Mr. Gerlitzky said that the media and law enforcement, emboldened by the Chabad leaders at 770, have exaggerated the impact of the January incident. “The whole story has been blown out of proportion,” he said, adding that many people in the Crown Heights community favor an expansion of 770, even if they do not condone excavations done without permits.

Contacted for comment, Rabbi Motti Seligson, a spokesman for the Chabad-Lubavitch movement, said, “Violence and destruction are anathema to everything the Rebbe taught. We pray that they see the error of their ways.”