The government has authorised only government hospitals to accept these notes from patients.
"In view of the hardship being caused to the large number of patients at private hospitals, we have made an urgent representation to the government that this exemption should apply equally, for payments, at private hospitals," Fortis Healthcare said in a statement.
The hospital is following up the matter with the authorities and hope the government will step in quickly to resolve the issue.
"The decision to allow Rs 500 and Rs 1000 notes only at government hospitals needs to encompass charitable and private hospitals and pharmacies as well," H S Chhabra, Chief of Spine Service & Medical Director, Indian Spinal Injuries Centre said.
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He said patients and their families in such hospitals are facing a crisis.
"I appeal to the government to look into their problem of these patients and to extend the relaxation it has made with regard to government hospitals to private hospitals too," he added.
In a major fight against black money, fake currency, corruption and terror financing, Prime Minister Narendra Modi last nigh announced demonetisation of Rs 1,000 and Rs 500 notes with effect from today.