In the present Online Salary Management System, the DI/s of your District is the DDO ( Drawing and Disbursing Officer). So he is responsible for deducting the Income Tax every month. He will issue Form 16 and he will file Return on quarterly basis with his TAN. Your HM should deduct Income Tax every month from every individual’s salary while preparing Online Salary Bill. As TDS is pending from last three months, he should deduct four months’ TDS in the coming month ( for example, if one’s TDS for a month is Rs.1000/-, the HM should deduct Rs.4000/- in the coming month, and Rs.1000/- every month after that) to adjust the previous TDS. All you have to do is to file individual Return with your individual PAN annually every year.