Rangin Dadfar Spanta lost the no confidence vote, which was conducted as a secret ballot, in the lower house of parliament today.
However, Afghan President Hamid Karzai says he will keep Spanta at the post until the Afghan Supreme Court rules on whether lawmakers have the legal authority to oust a minister for an issue that is not directly related to his ministry.
Iran says it has expelled nearly 50,000 Afghan unregistered refugees during the past month.
Spanta had urged Iran to suspend the repatriations because Afghanistan does not have the land, housing, or financial resources to help resettle refugees.
Spanta is the second cabinet minister to lose a no confidence vote over the issue. Refugees Affairs Minister Ustad Akbar Akbar lost a similar vote on May 10.