Late Filling of Income Tax Return

Hi, my father has a proprietorship firm, but since A.Y. 2008-09 he has not filling his income tax return, but now he wants to pay tax and return the file, but the concerning ITO is not ready to accept the A.Y. 08-09 file, saying is has already late hence my father need to go through CIT, through an application, 

but the thing is we don't know the application format and under which section it should be, i am looking for your help, and I'll be appreciate if some one can send the format to my mail id.  ellin860 @ gmail.com,

Thanks in Advance.

Regards

Ellin Gopinath