Israeli authorities said today they will presecute 41 ultraorthodox Jews of the Hasidic Mea Shearim quarter of Jerusalem for their role in clashes last night in which youths barricaded themselves in a seminary and hurled rocks, bottles and flares onto policemen in the street below.

The clash, in which 12 police officers and 30 demonstrators were injured, occurred when authorities went to the Toldot Aharon Yeshiva, or Jewish seminary, and attempted to arrest the ringleaders of an earlier rock-throwing clash on the controversial Ramot Road in northern Jerusalem.

Hundreds of ultraorthodox Jews, led by the militant Neturei Karta Hasidic sect, had hurled stones on Ramot Road in a protest against automobiles driving on the thoroughfare on the Sabbath, the Jewish day of rest when according to conservative Jewish tradition much activity is banned.

Neturei Karta is a small anti-Zionist group whose members believe Jews do not have the right to establish a state until the appearance of the Messiah. It regularly provokes confrontations with the police as a gesture of defiance of the government it refuses to recognize.

Police dispersed the earlier demonstration and then last night went to the yeshiva to arrest the organizers, most of whom are students, officials said. The Jerusalem police superintendent, Eytan Katz, said students hurled bottles and stones and ignited flares from the roof, and that police responded with tear gas.

The Neturei Karta spokesman, Rabbi Moshe Hirsch, called the clash a "police riot" and said members of Israel's border police indiscriminately smashed windows, destroyed furniture and damaged a synagogue. The yeshiva today remained littered with broken furniture. Scores of windows had been smashed.

Katz said most of the damage occurred when students erected barricades by piling furniture against doors and when police broke down the barricades to get inside.

Jerusalem Mayor Teddy Kollek criticized the extremist orthodox residents of Mea Shearim, who almost weekly have had clashes with police over the use of Ramot Road on the Sabbath. The entire Mea Shearim quarter is blocked off on Saturdays, but Ramot Road, which passes another Orthodox neighborhood, has remained open to traffic.

"A yeshiva that collects flares, stones and broken bottles for fights seems to me to be an extraordinary kind of educational institution," Kollek said.