in Kerela, it is due to certain circumstances(you can search "temple entry proclamation"), government has to intervene and handles administration of the temples. I think it's under communist rule these boards are formed. because, there was a revoultion in kerala happened 7-8 decades back which allowed equality of all hindus irrespective of the caste system. caste system menace was what may have triggered this managing of temples in kerala under government ministry. although, caste system is very less these days, government want to milk money from temples like Sabarimala,Guruvayoor which collects immense amount of wealth every season.
while for mosques,churches they are not preferring to choose government take over of administration. although funds,management of properties are tracked by minorities affairs ministry(state and central).
Government of India, Ministry of Minority Affairs - Home Page
Minority affaris minsitry monitors waqf activities. mostly headed by a muslim minister. current minister in centre is Adv. Salman Khurshid .