Media reports say order is part of preparations to evict Jewish settlers.
Up to 20 Israeli settlers and police were injured when Israeli police were dragging settlers out of the building which they have been occupying since March 2007.
The eviction was far less violent than anticipated beforehand.
“Once the Israeli security forces moved in it was all over in less than one hour,” Dan Nolan, Al Jazeera’s correpondent at the scene.
But soon afterwards, settlers fired live rounds at police and the media.
Hundreds of settlers’ supporters and activists flocked to the area in the past week in solidarity with the occupants and tensions have been high.
Around 200 people were inside the house at the time of the eviction.
The settlers claim they have lawfully bought the Hebron house from a Palestinian, who denies selling the house.
On November 16, the Israeli High Court of Justice ordered evacuation of the house until ownership is determined.
On Thursday morning, Ehud Barak, the Israeli defence minister, met settler leaders in a failed attempt to work out a compromise deal.
Barak said that the building, once evacuated, will be guarded by the Israeli army until the courts rule on its ownership.
Palestinians said on Thursday that Jewish settlers had sprayed graffiti on several
mosques in villages surrounding the city of Qalqilya. Some of the graffiti read “Regards from Hebron” and “Death to Arabs”.
The settlers are also accused of damaging Muslim gravesites and stoning Palestinian homes.
On Wednesday, the Israeli army declared the area surrounding the house a closed military zone and hundreds of police and army forces were deployed in Hebron.
Israeli military analysts said they feared the violence in Hebron could spread to other West Bank settlements as part of an organised uprising.
Thirteen settler families were living in the controversial house.
It is located in a key strategic location between the settlement of Kiryat Arba and the Cave of the Patriarchs, a holy site for Jews and Muslims.