KK has clarified the point. As regards Special allowance also the interpretation is that if the special allowance is an allowance paid in common to all employees it should be taken as part of statutory salary for all purposes. The same ruling applies here also. It is unfortunate that your management has taken a different view on salary to include only the basic pay.
A tag line from Madhu T K- A successful HR person is one who denies benefits to employee following the directions of the top management completely diluting the professional ethics. he is the person who is given appreciations from the employers and by that recommended by the employers for awarding Best HR Practices Award.
The above tagline is one which is taken from my own experience over the past 30 plus years. I have seen Management Associations giving applause to HR guys who do not know what the law stipulates and how the workers can be made happy and engaged by providing the best HR practices. He may be good in presentation on employee engagement, he may be excellent in English communication, but he may be a big zero in people management!
Regret to say that Neha's company HR belongs to this category. If your company management says that you will be paid only basic pay you should accept it. This is because in practice you cannot file a complaint before the appropriate authority and fight for justice. Though women are empowered, when it comes to a situation like this nobody will come for your help. In fact when the proposal for amending the Maternity Benefit Act came up, I had posted in this citehr itself that this will result in reduction in employment to women because the employers will not find it affordable to pay 6 months pay even though these employers may include women entrepreneurs. But once it is enforced it should be implemented and you cannot deviate from the law.
Anyway, you mat speak to the HR Manager over there and if he is not convinced, take a step either to fight for the justice or to accept what your company says!
Repercussions: If you take the first option of taking the issue to Labour Office, please ensure that you will get help from others including forums for women rights. Once you are through, you may get justice in the form of full salary during maternity leave days. I am not sure what will happen when the leave period is over and you resume to attend to your duties. They will not terminate you from service, that I am sure but I cannot give any guarantee about your rating in the coming performance appraisal. You may also anticipate a change in the work profile also.
If you opt for the second thing, you will be receding from your values and rights of a woman. That also is not right. But you can expect continuity of employment, fair appraisal, etc.
Think and act.