Israeli police have arrested a number of Jewish settlers during clashes in the Gaza Strip.
Police were ready for the protesters
Security forces dragged protesters out of buildings they had occupied in protest at Israel's planned withdrawal from the area.
In Jerusalem, police fired water cannon at protesters who blocked the main highway into the city during rush hour.
Meanwhile, an Israeli aircraft has hit a warehouse in Gaza in which Israel said Palestinian rockets were kept.
The aircraft fired a missile at the building in Beit Hanoun, causing damage but no reported injuries.
At sunset on Wednesday, police moved in to the Palestinian village of al-Mawasi to clear a building that had been taken over by radical young settlers and turned into a stronghold.
The area saw clashes earlier in the day when security forces fought with settlers who had dug themselves in in protest at the planned withdrawal.
Youths exchanged punches and kicks with soldiers, who dragged several of them away through the dust to an army vehicle.
Security forces also intervened after settlers and Palestinians began throwing stones at each other.
Israeli authorities are trying to stop settlers holing themselves up in abandoned buildings ahead of the August withdrawal.
The BBC's Alan Johnston in Gaza says that in recent weeks the territory's southern settlements have seen an influx of hardcore activists who are preparing for a confrontation with the army when the evacuation begins.
Protests also spread to Jerusalem, where dozens of youngsters dashed into the six-lane highway and sat down, at the height of the evening rush hour.
Police turned water cannons on the demonstrators to disperse them, and about 150 were arrested.
The authorities fear settlers could resort to violence
Protesters also spread oil and spikes on the Jerusalem to Tel Aviv highway.
The road protests have been called by an extremist settler group, while the main settler body has distanced itself from such actions.
Our correspondent says the protests are being seen as the opening exchanges in what may be a fraught Israeli withdrawal from Gaza, where there are 21 Jewish settlements.
Israel plans to evacuate over 8,000 Israelis and withdraw the troops who protect them as part of a unilateral disengagement from Gaza, which is scheduled to begin on 15 August.
Israeli Prime Minister Ariel Sharon vowed on Wednesday to "act with an iron fist against hooligans" who used violence to oppose the withdrawal.
On Tuesday, an Israeli soldier who refused to help demolish settler buildings in the Gaza Strip was sentenced to 56 days in jail in what is being seen as a test case of how the army will treat dissenters.