It is believed that your transactions with the company are verbal. You should issue a written communication, under proper acknowledgment, to the good offices of the company i.e. appointing authority, MD, CEO, Head-HR, Company Secretary, and the competent employee who issues salary slip and who has signed on your form 16, narrating all the incidences and may mention that you are being unnecessarily harassed and good offices should provide you the relief say within next 7 days or you should be constrained to initiate legal action at the cost and consequences of the company.
Has the company issued you the salary slip for all the months of your employment, form 16, FNF statement........? These should suffice to clarify the matter with I. Tax authorities. You may visit the I. Tax Commissioner in person and lodge a complaint and demand that a notice may be issued to your company as you have produced all proofs and default is at the end of the company.
What was the mode of disbursement of salary and other payouts i.e. bank transfer in your salary a/c in the bank, or by cheque/DD?
All payouts to the employee are disbursed in salary a/c in bank.
In your form 16 issued by the company, it is mandatory to mention the amount of tax credit with challan number.
If you have not received all the details, you may clarify the matter to the I. tax authority that employer is not issuing you the form 16, salary slips for all months of your employment.
You should lodge a complaint with jurisdiction authority C.I.T-TDS ( where the company files the return quoting TAN/PAN number of the company which are mentioned in form 16 and registered office address of the company) if the company has not supplied you the form 16.
If you are not able to handle the matter on your own you may visit a competent and experienced service/I. Tax lawyer with all records and proceed to issue alegal notice and subsequently legal action.