Hey,

You can appy for IISER in your final year of graduation but you need to meet few  requirements.

The eligibility for  Master's in physics  from IISER should be,

-a minimum of 60% in your graduation

-should have appeared for IIT JAM  and his or her rank should be under 500 .

Below is the link for eligibility bof IISER Pune,

http://www.iiserpune.ac.in/admissions/int-phd-programme

As you have not mentioned a particular IISER, so I have given you the reference of IISER Pune.

Hope that helps.

Thank you.