Hi! Thanks for the question!
To get the taxes paid in the last 6 years would not be an option as you should have objected before the taxes' cheques were issued.
If your school is duly registered with the concerned authorities as a charitable issue, you may move an application duly supported with the Registration certificate, PAN Card, ITR and whatever is demanded from the office, before the tax collecting authority. You have to establish that your Sanstha is a non-profit organization.
If you get entangled for the nominal rent that you are talking about, the returns would be difficult.
Regards!
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Till the time property is registered/occupied/used as "leased" it is liable to be charged with commercial rate of tax by the municipality irrespective of the fact that two of three floors are being used to dump your garbage and the only floor is used for running school whether the same is for charitable or non-charitable.
Consult a local lawyer for guidance on the provisions of GHMC Act.
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Yes, consulting a local lawyer to wind things up and also the registration withing the four walls of GHMC Act would be your way.