Israeli Prime Minister Benjamin Netanyahu condemned on Wednesday an assault on an ultra-Orthodox soldier by coreligionists in a religious neighbourhood of Jerusalem, vowing a tough line against anyone threatening army personnel.

"We will crack down on anyone who tries to terrorise civilians who are fulfilling their duty to the state," he said, following the incident on Tuesday night, which saw a soldier forced to hide in a building in Mea Shearim after a group of ultra-Orthodox hurled stones at him.

When the police came to rescue him, they too came under a barrage of stones thrown by a group of up to 150 people, a spokesman said.

Defence Minister Moshe Yaalon also denounced the attack, calling it a "despicable and loathsome incident" which needed to be dealt with severely.

"We must not permit such bullying," he said in a statement issued late on Tuesday which called on leaders of the ultra-Orthodox community "to condemn this violence and act forcefully to uproot this phenomenon."

The assault came as a national debate rages over whether to require the ultra-Orthodox to perform the same compulsory military service carried out by other Israeli Jews.

Currently, tens of thousands of them are exempt if they are studying in a seminary, but Israel is pushing through changes to the law which would end the system of exemptions.

The move is firmly opposed by the ultra-Orthodox community, which is not represented in government for the first time in decades.

"The best response to these lawbreakers is to increase the number of ultra-Orthodox conscripts," Netanyahu said, pointing to the government's approval on Sunday of a draft law which would require all ultra-Orthodox men aged 21 and over to sign up for two years of military or civilian service.

The bill, which would allow just 1,800 exemptions for seminary students, must pass three readings in parliament before becoming law.

Military service is compulsory in Israel, with men serving three years and women two.

Ultra-Orthodox Jews make up roughly 10 percent of Israel's population of just over eight million.