Thirty men were arrested overnight into Sunday morning as they protested the removal of graves to make way for a hospital expansion in southern Israel.
Police forces were deployed to Ashkelon city, where the graves are located, Saturday night to prevent the wave of angry protesters from interfering with the relocation. Demonstrators blocked several roads and burned down garbage cans.
The main opposition came from the Ultra Orthodox ommunity, fearing these are Jewish graves and removing them would be against their interpretation of Jewish faith.
Despite the protests, Prime Minister Benjamin Netanyahu ordered a go-ahead of the relocation.
"There is an important Ultra-Orthodox public who sees itself hurt by the decision but public welfare is the decisive factor," Netanyahu said at the start of the weekly Cabinet meeting Sunday.
Chief Rabbinate of Israel backed Netanyahu, but views vary among different sections of the Orthodox public.
According to the antiquities authority, the graves date to Roman and Byzantine era, and likely belong to idolaters who inhibited the area.
The Ashkelon hospital is the main medical facility in the Gaza area. It served Israeli civilians and soldiers during a conflict in January 2009, and has been in need of urgent expansion and missile protection.
The antiquities authority plans to hold a news conference at the site Sunday evening.
Relocation is expected to take up to three days.