Police spokesman Micky Rosenfeld told AFP that 1,000 ultra-Orthodox men were kept away from a large group of "Women of the Wall" activists conducting their monthly prayer using prayer shawls, after a court ruled they could do so.
"Police arrested three ultra-Orthodox men and detained another two" for public disturbances," Rosenfeld said.
Ultra-Orthodox men had tried to break through reinforced police lines and reach the women, some calling police holding them back "Nazis" and yelling offensive remarks at the women while others blew on whistles to drown out their prayers.
An AFP correspondent said they also threw bags containing liquid, water bottles, bags of rubbish, plastic chairs and eggs at the police and women worshippers.
Two police officers were lightly injured and treated at the site, but no women were hurt and they managed to complete their prayers, some holding flowers alongside prayer books.
When the prayer ended, police escorted the women to a bus which was hit by stones as it left the area, Rosenfeld said.