"Over the past few hours, dozens of protestors attempted to break into the Tel Hashomer base during protests that took place outside of the base", a military statement said.
The demonstrators "managed to infiltrate the Adjutant Corps Monument adjacent to the base fence" before being cleared out by police, it said.
Tel Hashomer, located east of Tel Aviv, is the largest base for newly enlisted army recruits in Israel.
The Israeli military said it "condemns this violent behaviour and insists that the protestors be brought to justice".
"The enlistment of ultra-orthodox citizens is an operational necessity and is being conducted in accordance with the law", and the military is "determined" to press ahead with it, the statement added
Historically exempt from compulsory military service, ultra-Orthodox seminary students are being called up while Israel's war in Gaza and a potential conflict with Hezbollah on the northern border sap resources and fuel resentment of those who do not have to serve.
The call-ups follow a ruling in June by Israel's top court that exemptions from mandatory service for ultra-Orthodox men were discriminatory and that the state must draft them.
Under longstanding arrangements, ultra-Orthodox Jews, who make up about 13 percent of Israel's 10 million population, had not been subject to the draft.
Members of the largely insular community, where young men of recruitment age typically study in Jewish seminaries, have taken to the streets to protest conscription, leading to clashes with police in Jerusalem.
Ultra-Orthodox men had already clashed with police outside Tal Hashomer on Monday before being dispersed or physically carried away.
In July, one leading ultra-Orthodox rabbi, Dov Lando, urged Yeshiva students to ignore the summons orders, writing in the Yated Neeman daily that it was "war" against religious Jews.
