Gift deed

Dear Law Experts, My father has gifted a property (Flat) in joint name of myself and my wife (which he purchased in early 1970s in Mumbai) and Gift deed got registered in year 2011. Since my father acquired this property along with other members from Collector through Social Justice and Welfare Department, Maharashtra, all the document has been sent to this department for necessary permissions. But Social welfare department does not have clause to transfer the flat in our name by Registered Gift deed. So the file is pending in Social Justice and Welfare Department, Maharashtra. My questions : 1) If other departments can transfer flat by Gift deed, then will Social welfare department transfer the registered Gift deed flat? 2) Shall I go to Court to get the order pass directing Government of Maharashtra to transfer the flat. 3) Any other solution like Will and Probate please?