Can i get home loan against my salary certificate if the land on which the house is intended to be built is disputed in court

But my father's grandfather had transferred the properties to my father through a registered gift deed when his son (ie my father's father had passed away). Does that not make my father the rightful owner of the property. My father's father was never the owner of these properties since he died young. My father's grandfather was the one who owned the properties and later transferred it to my father as gift. Hope this clarifies the situation and thanks for your answer.

As of now your father is the absolute owner of the property based on the Registered GIFT DEED executed by your father's grandfather.

If you approach the bank for loan on the basis of the said document, there should be no problem.  Currently, there is no case by anybody (including your Aunt) against the property or about the title of your father to the property.  In that scenario, there wont be any problem in giving loan against that property.  However, it will be loan against property (involving higher % of interest) and not HOME LOAN in your name.  Home loan can be given only to the one who is the owner of the property to construct the house. You want to take home loan on the basis of your salary certificate to construct an house on the property owned by your father.  BANK may not be willing to give the home loan to you since you do not own the land.

We have been planning to transfer enough land to my name so that we can get loan from bank. In that case there shouldn't be any problem right since the land will be in my name and I will be submitting my salary certificate too. As you said currently there is no case by my aunt, but what if she files a case before we could apply and get the loan from bank. Will the bank check if the property is in court case?

Whether or not the bank checks, you are liable to inform the bank.  

If you are really interested, why will you wait till your Aunt files a case against the property?

You seem to be revealing all facts point by point. You should have included all points in your query originally. Okay. When you approach the bank for housing loan, the documents they shall surely wish to see in original are:

1. Registered Gift Deed in favour of your father
2. Registered Gift Deed from your father to you for the portion of land on which you wish to construct house with housing loan from bank

If you are having the above documents, you may approach the Bank. Ultimately, what bank shall vierify is whether you have proper title deed in your name supported by documents.