A secure end-to-end communications system includes a vault controller based registration application for managing the issuance and administration of digital certificates for use in conducting electronic commerce in the system. The system includes an end user terminal and a registration authority terminal coupled to a vault controller through the system. A registration application executable in the controller utilizes SSL and dedicated vaults to process requests for digital certificates from end users on an automated or manual basis. The registration application includes an enrollment module which implements the process of applying for and receiving certificates; an RA desk top module which allows an administrator to review certificate requests and manage certificates; a master Registration Authority (RA) module which conducts the processing of requests and the generation of certificates; and an RA (Registration Authority) database serves as a repository of information about applicants, certificate requests, and their processing history.