The organisations said that 659 homes in the centre of Hebron had been vacated since the beginning of the second Palestinian intifada, or uprising, in September 2000.
Palestinian businesses were also suffering, the groups said, with 76.6 per cent in the centre of Hebron closed, 62.4 of them since September 2000.
At least 440 of those were shut after orders by the Israeli military.
The report says Palestinians have fled the town because the Israeli military has banned them from using the main streets of the city and enforced a number of curfews.
The groups say the army has also failed to prevent attacks on Palestinians and their property by settlers.
When contacted on Sunday evening, an Israeli government spokesman refused to comment.
Hebron is a holy city to Jews and Muslims.
It was the first West Bank town Jewish settlers entered after the area was occupied by Israel following the 1967 war.
They live in close proximity to the remaining Palestinians, sometimes building their houses on top of those belonging to Palestinians.
In 1997 Israel withdrew its troops from 80 per cent of the town but maintains a military presence there to protect the settlers.
All Jewish settlements, including those in East Jerusalem, are illegal under international law, though Israel disputes this.