RNA - Israeli border police arrived before dawn on Thursday and dismantled the protest camp, according to witnesses, Al-Jazeera reported.
Israel's plan to demolish the village, home to nearly 200 people, and relocate its residents has been criticised by Palestinians and drawn international condemnation.
"We hope that ... it will satisfy them that they succeeded in destroying the five houses. It was not our battle to fight, defending the empty houses. Our battle is to defend the houses of Khan al-Ahmar," Walid Assaf, head of the commission against the wall and settlements, told Al-Jazeera.
The predawn operation raised fears among residents that the demolition would occur soon, but the Israeli forces left the area after they removed the shacks.
"At 5am (local time, 02:00 GMT) this morning Israeli forces moved in. They stayed on the outskirts of the village, an area where there were a few temporary structures that had been put up by activists in solidarity," Al-Jazeera's Harry Fawcett, reporting from Khan al-Ahmar, said.
"They prevented access to anyone else as they demolished those structures and took them away," he added.
The Bedouin village is located in a strategic spot near Israeli settlements in the occupied West Bank and along a road leading to the Dead Sea.
The Israeli defence ministry body, which oversees civilian activities in the occupied Palestinian territories, said the five caravans had been pitched illegally over the past few days.
"The erection of these structures was advanced by representatives of the Palestinian Authority in protest and defiance of the decision of the (Israeli) High Court of Justice, and in opposition to the enforcement of Israeli law in Area C," the Coordinator of Government Activities in the Territories stated.
It was referring to the 61 percent of the occupied West Bank where Israel exercises full civil as well as military authority.
Last week, Israel's top court rejected petitions to prevent the demolition of Khan al-Ahmar, agreeing with Israeli authorities who said it was built without proper permits.
Palestinians say that the required building permits are impossible to obtain.
"Over there, there are a number of settlements allowed to grow naturally - the number of residents naturally - but here we are banned from doing a single thing," Abu Khamis, a village spokesman, said, adding that "that is racism, that is apartheid".
Activists say that continued settlement building in the area would eventually divide the occupied West Bank in two, dealing a death blow to any remaining hopes of a two-state solution.
On Monday, Britain, France, Germany, Italy and Spain issued a renewed call for Israel not to demolish the village, warning of the consequences for residents as well as "the prospects of the two-state solution".