بسم الله الرحمن الرحيم
(Fatwa: 22/18/SD=1/1439)
Paying more amount as deposit and giving less rent of the house is tantamount to benefit from debt which is unlawful as it is interest. In the question mentioned above if you are staying on the rent of 100 rupee monthly for three years by paying six lakh deposit amount then you should ask the owner to forgive the standard rent of three years and in future deal with him on the basis of standard rent. If he does not forgive you then it shall be mandatory for you to pay the standard rent of the house whether you get it deducted from the deposit amount or leave the deposit amount with him and pay the rent separately.
Allah knows Best!
Darul Ifta,
Darul Uloom Deoband