I want to know the Total number of NGO/NPO registered across the country, can I file RTI for this?
By way of some judgments passed by the Central Information Commission (CIC), NGOs receiving substantial grants from the government directly or indirectly have been brought within the purview of the RTI Act. This includes private NGOs as well which receive substantial grants from the government. You could address your application to the ministry dealing with NGOs (home ministry, ministry social justice)
You could also access the list of NGOs from http://ngo.india.gov.in/ngo_stateschemes_ngo.php
For the list of private NGOs, you would have to approach the multiple offices of societies where NGOs are registered.