@ S. Shiroor:
He is just not aware about anything relating to taxation. So there is no point of him going to the AO and ask the details. You are stating it because you know all the pros and cons., so you can speak to the AO but think from his angle, he is not even from commerce background and also does not know much abt taxation matters also. Any discrepancy if the AO will find then he won't be able to handle it. It is always advisable to take the help of an expert (here I mean CA) before the things worsen up more. Just because he is a Govt officer, that does not cover up the mistake that he has made. You are trying to encourage him but this is just not the correct way. "Don't take the pills without doctor's advice" as the quote states. In similar manner, everything cannot be done on your own, you need to rely upon an expert for the problem to get resolved.
@ Bharath:
Take the help of a CA. When you will give the CA, necessary details he will take an appropriate action. Comments provided here by every member including me won't be working since the exact facts are still not clear as to
What kind of income did you show as your income in your Itr?
Which ITR have you filled up?
Who told you to pay Self Assessment tax?
And you cannot file revise return as it is a belated return. Now that you have done this all, please take all the returns that you have filed, your bank statements and SA tax challan with you to a CA and tell your problem to him. I know you may have not done with a wrong intention but definitely it's your mistake that you did unknowingly and due to lack of knowledge in taxation matters.
So in order to avoid any further problems, consult a CA.