Overide the Act??

i have a simple question...

Can the Income Tax Department do anythin which is not mentioned in the Income Tax Act

eg.an assessee has to pay Rs.50,000 for AY - 2010-2011 and is to recieve refund of Rs. 75,000 for AY 2011-2012 . Can the IT Dept set-off the amounts and pay the refund of only Rs.25,000 ??

assuming both the returns are filed on 20-6-2011 and the assessee has not paid the income tax for AY 2010-2011 .