"Provincial governments have taken in their control management and administration of 182 seminaries (madaris)", the ministry said in a statement, referring to religious schools.
What to do with madrasas is a thorny issue in Pakistan, a deeply conservative Muslim nation where religious schools are often blamed for radicalisation of youngsters but are the only education available to millions of poor children.
The interior ministry said other institutions from different groups had been taken over, including 34 schools or colleges, 163 dispensaries, 184 ambulances, five hospitals and eight offices of banned organisations.
Many banned groups such as JeM run seminaries, which counter-terrorism officials say are used as recruiting grounds for militant outfits