The Higher Arab Monitoring Committee, which represents Arab communities in Israel, had called for a day of "angry strikes" including demonstrations in 15 cities to denounce the plan.
Arab Israeli MP Jamal Zahalka said more than 1,000 attended in the main demonstration in Beersheba.
"We called for a peaceful protest in which more than 1,000 people took part but the police used force. They tried to beat a girl with clubs but when I tried to protect her they beat me up as well," Zahalka told AFP.
Fifteen protesters were detained following the clashes.
The security forces also detained 14 demonstrators among hundreds who blocked a road and threw stones at them in Sakhin Town, said police spokeswoman Luba Samri.
Later in the evening about 100 protesters demonstrated in Arab east al-Quds (Jerusalem) outside Damascus Gates, one of the doors to the Old City.
Some demonstrators hurled rocks at police and at least one protester was arrested, an AFP photographer said.
Organizers said the overall number of protesters who took to the streets in Beersheba, the southern Negev desert region, Galilee in the north and Jaffa near Tel Aviv could have been in the thousands.
The resettlement plan was approved by the Israeli regime in January and by the parliament in a first reading in June. Two more votes are expected.
The plan call for the relocation of 30,000-40,000 Bedouin, the demolition of about 40 villages and the confiscation of more than 700,000 dunums (70,000 hectares) of land in the Negev.
The regime has said it would "as much as possible" grant legal status to Negev villages that are currently unrecognized by the authorities if they met a minimum population criteria. But those criteria have never been stated.
A cabinet statement has said "most" residents -- who do not currently receive government or municipal services -- would be able to continue living in their homes after the villages are granted legal status.
There are about 260,000 Bedouin in Israel, mostly living in and around the Negev in the arid south. More than half live in the so-called unrecognized villages by without utilities and many also live in extreme poverty.
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