Tax deducted at source and yet not paid is a serious offence for which employer is liable for prosecution under sections 406 and 409 IPC apart from under IT Act. See decision of Calcutta HC of 2003 in Sushil v State. Give a legal notice to employer on this line and he will hopefully comply with and pay your dues. Since you are governed by Bombay Shops and Establishment Act, you could have complained to Inspector under the Act for payment of your dues. But under section 61 there is limitation period of three months for making complaint to magistrate for non payment of wages etc otherwise you have to explain delay. If you covered under definition of workman then recover wages under that Act, if you are not able to recover under the earlier method suggested.
Sushil 22nd February 2015 From India, New Delhi