Foreign Office spokesman Nafees Zakaria said the restrictions were in response to Pakistan awarding the death sentence to Indian national Kulbhushan Jadhav.
A letter of recommendation by Pakistan Foreign Affairs Advisor Sartaj Aziz will enable a Pakistani national to get a medical visa for India, the External Affairs Ministry had announced in May.
"It is highly regrettable that India has placed such restrictions on visas for patients who are suffering from serious and terminal illnesses. Asking for a letter from the Foreign affairs Adviser is against the diplomatic norms," Zakaria said.
Zakaria also accused India of not taking action against those involved in the Samjhauta Express attack.
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He said the USD 50 million blocked by the US was not aid but reimbursement of what has actually been spent by Pakistan on counter terrorism operations.
Earlier on July 8, External Affairs Minister Sushma Swaraj waived the condition of a letter from Aziz for an ailing PoK resident to get a visa and said he would be allowed to come to come India as Pakistan-occupied-Kashmir (PoK) was an integral part of India.
"POK is an integral part of India. Pakistan has illegally occupied it. We are giving him visa. No letter required," Swaraj had tweeted.
India's decision to impose restrictions on medical visas for Pakistani nationals came in the wake of growing tensions between the two countries.