i am using a certificate generated by makecert which has both private and public key. The java side uses this public key to encrypt the data and .net decrypts it back.
I stumbled across this page when I was trying to find examples of makcert usage with x509 certificates and rsa using c#, and unfortunately it only provided part of the solution. I put all the bits together in a blog entry that people might be interested in, and it can be found here: http://nick-howard.blogspot.com/2011/05/makecert-x509-certificates-and-rsa.html