Difference in income as per form 26as and form no. 16

Hi,

I have to file ITR of Mr. P working in a Private Company. His salary as agreed was more but actual payment made to him was less than the agreed salary due to financial crisis in the Company.  The Company has deducted TDS on salary considering FULL PAYMENT and the same is also remitted to Govt.  In Form No. 16, the Company has shown AMOUNT ACTUALLY PAID TO HIM AS his Income against salary.  Whereas in Form 26 AS downloaded from IT site, it is seen that the amount shown as PAID is more that the amount shown in Form No. 16.  Considering actual payment made to him and which is correctly shown in Form No. 16, there is excess payment of Income Tax and he is eligible to claim Refund.

 Please let me know whether there will be any problem or query from IT department in this regard as there is difference in amount paid as salary as per Form No. 26 AS and Form No. 16 issued by the Company.

Ex.  a)     Total Amount paid as seen in Form No. 26 AS                             Rs.  5,73,251.00  ( F.Y. 2012-13)

        b)     Actual amount paid to him and shown in Form No. 16

                issued by the Company                                                                Rs. 3,20,000.00

TDS deducted by Company on income of Rs. 5,73,251.00  Rs. 64,000/-

Tax payable on actual income as per Form No. 16              Rs.   6,500/-

Excess amount deducted and remitted                                 Rs. 57,500/-   which is to be claimed as Refund.

I HAVE TO ADD ONE MORE INFORMATION MR. P HAS LEFT THAT COMPANY AND JOINED ANOTHER COMPANY DURING THE SAME FINANCIAL YEAR. AND THERE IS NO QUESTION OF PAYMENT OF DIFFERENCE AMOUNT BY THE COMPANY AS THE ACCOUNT IS ALREADY SETTLED.    Please guide me considering the additional information.

 Vilas