You have been depositing the rent to Rent Controller which shows your bona fides. Nothing else could be done.

1) THE WAQF PROPERTIES LEASE RULES, 2013 have been framed by central Govt

2) A lease for any period from one year to 30 years of any immovable Waqf

Property shall be granted only with the prior sanction of the Board.

3) (21) Payment of Rent: All amounts payable by the Lessee to the Lessor

pursuant to this Lease shall be deemed to be Rent and shall be payable and

recoverable as Rent in the manner provided and the Lessor shall have all rights

against the Lessee for default in any such payment as in the case of arrears of rent.

Rent shall be paid to the Lessor without deduction or set-off, at the address of the

Lessor or to such other person or such other address as the Lessor may from time to

time designate in writing.

4)the

Mutawalli or the Board shall while granting the sanction for lease or renewal

thereof, review the terms and conditions on which the lease is proposed to be

granted or renewed

5) he Lessee’s obligation to pay Rent shall survive the

expiration of earlier termination of this Lease

6) you have to pay rent to mutalwali

7) The rent tendered by the lessee on time but refused by the Lessor in

accepting or giving receipt, may be deposited before the concerned Waqf

Board. The rent shall be treated as validly deposited if deposited by the

lessee within 15 days of such refusal by the Lessor.

8) instead of depositing with rent controller better deposit with wakf board as provided under the wakf rules 2013

Even if it is the property under the control of Wakf board, it becomes your duty to pay the rent to the Muthavali or any person named as in charge to collect the rental payments. In the absence of no such person you had been paying the rent with the court , this confirms your tenancy. If at all there is a claim by the wakf board to vacate you, they may have to approach court for evicting you by due process of law but they do not have any reason to vacate you since you have not defaulted the conditions of lease neither have defaulted in the rental payment.

My question is that whether paying rent to Rent control against this Wakf property is valid in this case and if not what should be the way to avoid any trouble? Kindly suggest appropriate legal way to this issue.

Since there is no one to receive the rental amount from you though you were desperately searching for the proper and authorised person to collect the same, you had no other option than to deposit the rent with the court which confirms that you have not done any offence by not paying the rent due to which you are liable to be evicted.

Your tenancy rights are very well protected so long you have defaulted the rental payment.

yes it is valid, court is the custodia juris of the waqf property.