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

There are lot of issues involved.

However, it is only the Bank concerned which will be in a better position to say whether they are willing to advance the loan to you or not.  Better get in touch with the Banks.

Whenever anybody approaches a Bank for Housing Loan, the documents (copies) relating to the property need to be shown to the Bank. Banks refer the matter to theri Panel Advocate for Legal Scruity of these reports and for confirmation that the said documents are in fact in the name of the person named therein.

In your case, you are informing on one hand that the land is disputed and in the second para of your query, you are noting that as of now there is no case and your aunt is likely to file a case

Basically, it appears you do not have any title deeds in the name of your father, in which cases Banks may not be coming forward to finance for housing loan. Salary certificate is not a basic qualification for taking Housing Loan. It is only a source which you can show that you are capable of repaying the loan. The basic document for housing loan is a title deed in your name or a document which on effecting sale shall be registered in your name to the satisfaction of the Bank.

On one hand you are talling that there is a sale deed in your father's name and in your original query you are mentioning that your father has no Pattayam document. Was it an ancestral property? If it is an ancestral property and there was no proper Registered Settlement Deed, it is open for dispute. Again now you are disclosing that your father has a sale deed but does not have title deed. If your father has a sale deed, are you informing that the land is his self acquired property? In which case, how your Aunt can contest it?

Please give facts properly. Further, based on your confusing disclosure of facts, it is not possible to give any clarification.

Okay now matter is clear. Apparently, your Grand Father died intestate ie. without writing a Will. In the absence of Registered Settlement Deed among the family members, your Aunt can litigate the matter and file a case in Court for proper settlement. In the legal scruitiny these issues shall come out and once the Lawyer discovers that the property is ancestral, heshall ask for further documents.

Sorry to say, you are unlikely to get Bank Loan based on this property.

You cannot confuse more than this!

If the property is (was) in the name of your father's grand father, and when your father's grand father was alive when your grandfather expired, being the owner of the property, your father's grandfather has every right to do whatever that wants to do with the property.  In that right, if he had given the property (GIFTED by Registered Document) to your father, that is perfectly legal and OK.  Nobody (including your Aunt) can object or question that or lay any claim over the property. 

What is required to be clarified by you is whether your father's grandfather gave the property to your father through REGISTERED GIFT DEED or not.  IF YES, then your father has perfect title to the property.  IF NOT, your father cannot claim exclusive ownership of the same.