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If you discover that there is a mismatch in Forms 16 and 26AS at the time of filing your ITR, then you can file it on the basis of the TDS deducted as shown in the salary slip or Form 16. Along with that, you must also bring the discrepancy to your employer’s notice. If the issue is not resolved, say within 30 days, you can write your grievance to your assessing officer to explain your case.
On administrative grounds, normally, the lower authorities will not give credit for the TDS not paid by the employer.
As per the income tax rules, it is the duty of taxpayers to pay any shortfall in tax liability. Therefore, if the department sends you an additional tax demand notice, i.e., 143(1) after filing the ITR (despite you pointing out of non-deposit of your TDS by your employer), you will have the option to file an appeal to the Commissioner of Income Tax [Appeals]. The commissioner will decide the case on the basis of the facts of the case. If you do not wish to appeal, then your only other option is to pay the tax demand yourself.
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