Police in Dimona on Monday evening arrested two Beduin men, a 47-year-old and a 51-year-old, on suspicion of vandalizing the Avdat National Park in the Negev on Sunday night.
The men denied involvement in the incident which left hundreds of archaeological artifacts at the UNESCO World Heritage Site severely damaged.
The suspects will be brought before the Beersheba Magistrate's Court on Tuesday for a remand extension hearing.
Police launched an investigation on Monday morning after church pillars at the ancient Nabatean City in the Negev were knocked down, stones and scripts were smashed, the altar was severely damaged and the walls of the compound were spray-painted.
Nili Dvash, the manager of the Avdat site, told Army Radio about the situation at the scene several hours after the place was vandalized.
"We saw broken arcs, broken walls that were dismantled. A lot of spray paintâ€¦ It looked like [the aftermath of] an earthquake, just vandalism for vandalism's sake," Dvash told the radio station.
Eli Amitai, director general of the Israel Nature and Parks Authority, said that the authority would work to immediately fix the damage and return the site to its previous state.
"This is irreversible damage to a site of national and worldwide importance - and with no reason. We will do everything to ensure that the police catch these criminals," Amitai vowed.
Among other leads, police were investigating whether the incident was related to the razing of 23 illegal Beduin structures in the South.