No problem, it can manage it for few months, good to migrate at the earliest. 

check this link 

https://www-secure.symantec.com/connect/forums/can-sepm-mr4-mp2-server-manage-sep-ru5-client

Once they are communicating to the proper server, in this case the MR5 server, just need to assign the package to the group and the "auto-update" will upgrade your clients to the proper client package/build.

Have you already moved your clients over?  Chaged the SYLINK.XML file using the SYLINKDROP tool?

SEPM and SEP clients are reverse Compatible. MR3 can report to SEPM MR5 however there will be some minor errors that you might find in the logs but nothing major.

However I would suggest to upgrade your Setup to atleast RU6a as there are many issues in MR3.

Hi Por,

The SEPM and SEP clients should be able to communicate without any trouble.  Here is the official article on the subject:

Does Symantec Endpoint Protection Manager function with different versions of SEP client? (http://www.symantec.com/docs/TECH131718)

My personal recommendation would be to upgrade both SEPM and SEP clients, though. MR3, in particular, is quite old. Migrating to RU6 MP1 will ensure that you are taking advantage of literally thousands of available fixes, enhancements and improvements.

Thanks and best regards,

Mick