The information leaked to the group shows that in three out of every four settlements in the West Bank at least some of the construction was completed without proper permits, Israel's Haaretz newspaper reported.
The daily said the database showed that, in more than 30 settlements, extensive construction of buildings and infrastructure like roads, schools, synagogues, and even police stations was carried out on private lands belonging to Palestinians.
In one settlement, Elon Moreh, 18 houses were built on private land, the reports says. In another, Efrat, a park and a synagogue were built on privateland, and in a third, Ariel, a college was built without legal approval.
Yesh Din said it would begin running advertisments in Palestinian newspapers to encourage people to take legal action, and will also offer legal counsel, the statement from the group said.
The database focuses on the 120 West bank settlements that have been authorised by the Israeli government since it occupied the territory in 1967. About 100 other unauthorised outposts have also been established by settlers.
The settlements are illegal under international law and the so-called "road map" setting the course for Israeli-Palestinian negotiations calls for a halt to their expansion.
There was no immediate comment from the Israeli government on the conclusions of the report.