What an Employee can do in Case of Non - Timely Deposit by the Employer
A taxpayer can preserve his salary slips at least till the time he gets tax certificate. Then if form 16 is not received, he can file his returns on the basis of salary slips (as TDS deduction by employer is mentioned in it). So, employee can get his claims even if the form 16 is not available. An employee need not worry about paying taxes again on his income only to get form 16 from the employer.
In case of e-filing, TDS certificate number is not compulsory.You can file your return even without TDS certificate if you know the TAN of your employer, which can be obtained from last year's Form 16 too.The situation would have been different when employer had not deducted TDS from your salary. In that case you were responsible to make payment of advance tax/tax as the case may be.
In the present case if your retun will fall under scrutiny, your employer will be prosecuted and he will be liable for interest and penalty and not you.