Protesters have held a series of demonstrations in recent days over the environmental scheme in southern Israel's arid desert region, posing a thorny challenge for the fragile coalition government.
Bedouin, who are part of Israel's 20 percent Arab minority, have long opposed tree-planting initiatives in the Negev, blasting them as a de facto government land grab in areas they call home.
"Police dispersed the demonstrators who blocked a road in the Negev and threw stones at the police," the security forces said in a statement.
Thirteen people were arrested in the events, the statement added.
An AFP photographer was lightly injured during the clashes.
The latest unrest in the decades-long dispute has attracted fresh attention given the make-up of Israel's coalition government, led by right-wing Prime Minister Naftali Bennett.
Bennett's government counts on the backing from the leader of the Islamist Raam party, Mansour Abbas, whose core political support comes from Bedouin in the Negev.
Nearly half of Israel's 300,000 Bedouin live in unrecognised villages in the Negev.
Abbas told Israel's Channel 12 news on Tuesday that his party will not vote with the coalition unless the tree planting is halted and formal negotiations with Bedouin leaders are launched to seek a compromise.
On Wednesday, Social Affairs Minister Meir Cohen said that a "compromise" had been reached that would allow for "accelerated negotiations" to take place.
But clashes have continued.
The right-wing Regavim environmental group called on Bennett's government "to take a firm position against the Raam Party's threats" and to ensure tree-planting projects continue.
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