Hi rahul,
What you can do is that you have to report the above facts to your employer. What your manager is doing is a wrong thing. No manager has a right to take the salary of the workers. What they are doing is a criminal offence. They are liable for forgery. If any one of the said workers gives a compliant then you will also liable as an HR executive. Even your employer will also be liable for the same. The best thing you can do is that you have to inform the same to your employer.