Two women settlers were detained and a third was slightly injured in a scuffle with soldiers, police spokesman Shlomi Sagi said on Wednesday.
The security forces were building a 25 metre-long, 4.5-metre-high barrier around the Palestinian house which overlooks the Jewish enclave of Avraham Avinu in downtown Hebron.
The house was emptied on Israeli army orders shortly after the outbreak of Israeli-Palestinian violence in September 2000.
The settlers also stoned several Palestinians, witnesses said.
In one incident, a Palestinian who had been stoned began scuffling with soldiers and police. He was wrestled to the ground and handcuffed before being driven away in an armoured jeep.
Settlers, many of them young children, tried to block construction of the concrete wall by sitting astride it before being dragged away by troops and police.
Police have maintained a regular guard to protect the home against attacks since a Supreme Court ruling reversed the army order, allowing Palestinians to return to the building. It is undergoing renovation and is not inhabited.
Clashes between Palestinians and
Jewish settlers are frequent
Last month, masked settlers injured a policeman as he filmed them attacking the building with sledgehammers.
In Wednesday's pre-dawn operation, the security forces took no chances, sending several hundred troops and police to the site, Sagi said.
As part of interim peace accords, Hebron, a city of 130,000 Palestinians, was split into two parts in 1997.
The downtown area remained under Israeli army control, while the other part was handed over to Palestinian control.
About 500 Jewish settlers, many of them ultra-nationalists, live in the Israeli-controlled part. Clashes between settlers and Palestinians are frequent.
On Tuesday, Israeli troops beat five unarmed Palestinian traffic police in the city when they refused to obey soldiers' orders to leave an area which the military said was off-limits to them.
Hebron's Palestinian police chief, Awni Samara, said the policemen were in the Palestinian-controlled zone and were not violating any agreements with Israel.
Since the latest round of Palestinian-Israeli violence erupted more four years ago, Israeli troops have moved in and out of the Palestinian controlled areas at will.