The ministry "heard objections" from the Palestinians and from residents to the plans to build a visitor centre just outside Jerusalem's Old City walls in the Arab neighbourhood of Silwan, a statement said.
However it approved the project on the grounds that it "will show important archaeological discoveries to the public".
"As a tourist attraction, this will contribute to the development of the city of Jerusalem," the ministry added.
It would be managed by Elad, a hardline settler organisation which seeks to increase Jewish settlement in east Jerusalem and which runs the nearby City of David archaeological site.
The Silwan neighbourhood is already home to dozens of Jewish settler families who live under heavy guard among their Arab neighbours.
Arab residents charge that the new visitor centre fails to take account of their needs and is an attempt to further strengthen the Jewish presence in Silwan.
He told AFP the new complex would be a multi-level building of some 172,160 square feet.
The decision came as Israel looked for ways to punish the Palestinians for applying to adhere to 15 international treaties after the Jewish state failed to release Palestinian prisoners.
Each side blames the other for breaching understandings that enabled the relaunch of US-brokered peace talks last July, which are now on the brink of final collapse.
