relief under section 89

Sir

   I am in govt. service and i received third instalment of my sixth pay commission arreer of Rs.60000b in the f.y. 2010-11.relating to previous years I claim  relief for arreer u\s 89 but my head of department did not allowed the same. What can i do? Can I.T. department will allow same when I file return for the F.Y. 2010-11. 

please answer at your earliest and thanks in advance.