If you are looking at the legal validity of the employers actions, the following regulations will apply.
1. The terms of appointment that was there when you joined.
2. Changes to the terms of employment that you agreed to (including deemed acceptance by continuing to work or not replying that you do not accept the terms). However, this means it must be explicitly communicated to you.
3. If the organisation has more than 50 employees at that location, the Standing Orders will apply. In that case, none of the HR Policies or procedure can be contrary to the standing orders, though they may be more favourable to the employees. This will never be allowed in standing orders.
Now, if it is a small office, standing orders do not apply, then obviously, you need to see whether you were informed of the changes. If not, the deduction is invalid. if standing orders apply, then the deduction is invalid anyway.
If your salary is below ₹ 18,000, then you are also covered by Payment of Wages act, under which such deduction is illegal.
Now what option you have?
You can go to the local Labour Commissioner and complain, He may help you unless you are at managerial level
You can go to a lawyer and have him issue a notice to the company. many times the notice is enough to make the company do the right thing.
You can also go to the labour union, NGOs or political parties who may help you. but in each case, there is a cost, which is basically the company will give negative BVG reply when your new employer calls to check your employment history.