The concept of beneficial ownership of shares finds its roots in Section 90 of the Companies Act, 2013 (“Companies Act“). Section 90 seeks to provide that the Central Government may appoint one or more competent persons to investigate and report as to the beneficial ownership with regard to any shares or class of shares.
Mini Raman in her article on Mondaq discusses about the law pertaining to significant beneficial owner in companies in her article http://www.mondaq.com/india/x/