Employee credited +10 tds by mistake-climed rfnd by him-dept

An employee of an organisation was credited 1000 extra by mistake . That employee claimed the same in his IT return.   

Later the same was corrected. Now the Dept. has sent notice asking the employer to file a correction return as they could not give credit to that employee because the amount ees not transferred to his account.

Under these circumstances what should the employer do....!!!  (The employee is rady to accept that he need not get 1000 as claimed in his IT return.)

Advise.  

(what ees this over..akshion by the Dept.)