The group was formed as an offshoot of the messianic Zionist movement Gush Emunim, and is run by Ze'ev Hever, a convicted terrorist.
The Israeli government has helped Amana set up new headquarters on the land, Haaretz reported, without informing the Abu Ta'ah family that their land was being expropriated.
Officials have been accused of redrawing existing property maps and hiding vital documents from the property's owners.
Speaking to Haaretz, head of the family Abu Ta'ah said: “We knew all my life that we had this land. When my mother was supposed to receive her National Insurance Institute stipend, they told her she would not receive it because we have land.
“Why is it forbidden for us to build while they are permitted? They are not the owners and I am. There’s no justice.”
In 2005, Amana handed over 913,000 shekels (£168,000) to the Israeli government for the use of a large swathe of East Jerusalem land which the state had first expropriated in 1968.
But in 2009 an additional 3000m² of land, which the Ta'ah family says belonged to them, was reportedly secretly added to the construction plans.
Development of new Amana headquarters has since begun on the site, protected by Israeli police. A petition by the family has been rejected by the Jerusalem District Court
In an investigation earlier this year, the Israeli government's own fraud squad found that 14 out of 15 transactions carried out by a subsidiary of Amana were fraudulent.
Amana-owned company Al-Watan forged documents and staged handovers of cash to stooges posing as Palestinian land-owners, to make it appear that they were legitimately purchasing land rather than forcibly seizing it.
Under a law originally introduced by the British administration in 1943, the Israeli government is entitled to expropriate any private property for governmental or 'public' purposes, often without compensation. In practice, the power is used to seize land belonging to Palestinians and build homes for Israelis.