A bill has been introduced in parliament that would resettle the Bedouin in the Negev, a southern desert region.
Protesters said they are determined the legislation will not pass, Ynetnews reported.
"The state of Israel wants to expel us from our homeland and we will not have it," one said.
Hundreds of people rallied at Hura Junction in the Negev, blocking roads. Protesters threw stones at police who responded with tear gas and stun grenades.
There was violence in Haifa where about 1,000 people turned out, and at a smaller rally in Jerusalem.
Dozens of protesters were arrested around the country, police said.