Urgent- Unlawful penalty on retention of government residence

Sir, My father is a Joint Director in sugarcane research center, Kashipur, distt- U.S.Nagar, which regulates under pantnagar university, distt- U.S. Nagar. He is currently residing in Pantnagar which is 60km from kashipur. So my father use to up-down daily from pantnagar to Kashipur (office). He has also allotted govt. residence in his station(Kashipur) but its unsafe to live due to its ill maintenance condition. My father got notice in the mid of 2015 to vacant pantnagar residence as he was allotted same residence in Kashipur. Then father wrote letters to estate officer of university to repair the house before we get shifted. But no response is given by Estate officer and even no repairing activity performed. My Father keep requesting for repairing but unfortunately in 2016 he suffered from chronic heart disease and undergoes angioplasty 3rd time. Then he forwarded file to Estate officer, requesting to stay in same place due to medical condition. File took time to processing. At last after completion of file processing in 22-05-2016 again notice came to vacant the residence and mentioned penalty (including rent) of around Rs 52000 per month to be cut from the date of month of 2015 when notice first issued. Infacts, normal residence rental charges are deducted from my father salary since 2015. Instantly notice reflects deduction of rent from 2015. So, during the period when file is in process and no action taken to repair house, how much its lawful to deduct charges from that period. Secondly, how its possible for government servant to pay huge penalty from his salary? Is the amount of penalty is lawful. My father also approaches to court to get stay order but nanital high court is close till 30th may. From 1st april onwards penalty is going to deduct from salary. It seems we have no option left as doors of judicial system also closed for us.