Generate SSL cert with stronger signature algorithm such as RSA-SHA 1 or SHA 2 from Certificate Authority Version: 5.2.3790.3959

We have a Certificate Authority (Version: 5.2.3790.3959) configured on  Windows 2003 R2 server in our environment. How do i generated SSL cert with stronger signature algorithm such as with SHA1 or SHA2

Currently i am only able to generate SSL cert with md5RSA.