I solved the issue by completely discarding the NPPAPI plugins and instead I designed WCF based web server. My requirement was that I needed to access windows registry, file system etc and to establish a communication channel with a process running on my machine for exchanging the messages. Earlier I used to install an NPPAPI based COM plugin which will do it all for me. With diminishing support for NPPAPI, I had to look for some other way.
I designed a WCF based service which is exposed as Web Server console application. I install this application on the machine and communicate with this through Ajax calls. It's cross domain communication so I need to set proper headers in the call request/response.
As the service is encapsulated in a web server console application , I can communicate with it through XHR.