The accident in Givat Zeev, just north of Jerusalem, raised more questions about safety measures at large ultra-Orthodox events, two weeks after 45 pilgrims were crushed to death in a stampede at the burial site of a Jewish sage in northern Israel.
A police spokesman said 650 worshippers were at the Givat worship site for the start of the Jewish holiday of Shavuot.
The event was held in a partially constructed synagogue. The local mayor and senior fire brigade and police officers said it had gone ahead despite the lack of a permit and official warnings that the building zone was unsafe.
A spokesman for the Magen David Adom ambulance service said at least two people were killed. Ambulances and military helicopters ferried the injured to hospitals.
Security footage broadcast on Channel 12 TV showed a crowded grandstand collapsing and worshippers falling on top of each other.
"We were called again to another event where there was negligence and a lack of responsibility. There will be arrests," Jerusalem District police chief Doron Turgeman said from the scene, on live TV.