Millions of lives are at risk in Iran because western economic sanctions are hitting the importing of medicines and hospital equipment, the country's top medical charity has warned.

Fatemeh Hashemi, head of the Charity Foundation for Special Diseases, a non-government organisation supporting six million patients in Iran, has complained about a serious shortage of medicines for a number of diseases such as haemophilia, multiple sclerosis and cancer.

Sanctions over Tehran's nuclear programme are not directly targeting hospitals but measures imposed on banks and trade restrictions have made life difficult for patients, according to Hashemi, the daughter of former Iranian president Akbar Hashemi Rafsanjani. Two of her siblings are in prison on separate anti-state charges.

"More than anything else, we have a lack of medicines for patients suffering from cancer and multiple sclerosis," Hashemi told the conservative website Tabnak. "Those with thalassaemia or in need of dialysis are facing difficulties too – all because of sanctions against banks or problems with transferring foreign currency."

Iran's central bank, the only official channel for Iranians to transfer money abroad, is a major target of the sanctions. Ordinary Iranians, including academics thereforehave no way of paying for services overseas, such as booking a hotel or subscribing to international journals.

Although foreign providers are not legally bound to refuse services to Iranians, they err on the safe side for fear of getting into trouble. Many Iranian Britons or Iranian Americans living in the west have complained they have had their credit accounts closed even though they have no connection with the Iranian regime or, in some cases, when they are allied with the opposition.

In midsummer, Hashemi wrote to United Nations secretary-general Ban Ki-moon calling on him to intervene for the health of Iranian patients who, she said, have had "their basic human right" taken away from them because of sanctions.

Earlier this month, it emerged Ban had warned the UN in a report that humanitarian operations in Iran were being harmed because of sanctions.

"The sanctions imposed on the Islamic Republic of Iran have had significant effects on the general population, including an escalation in inflation, a rise in commodities and energy costs, an increase in the rate of unemployment and a shortage of necessary items, including medicine," he said.

"The sanctions also appear to be affecting humanitarian operations in the country," he wrote. "Even companies that have obtained the requisite licence to import food and medicine are facing difficulties in finding third-country banks to process the transactions."

Mozhgan Elmipour, the mother of a four-year-old Iranian girl who was brought to London from Tehran for a life-saving surgery on her oesophagus, said: "Iranian hospitals have serious difficulties because of sanctions and not everyone in the country is as lucky as my daughter to be able to afford to come here."

Rojan Pirsalehi, whose oesophagus was damaged after swallowing a battery at the age of two, is being treated at Great Ormond Street hospital in London.

Her parents could not afford to bring her to the UK but thanks to a media campaign in Iran and help from the Iranian government enough funds were raised. The UK government facilitated her journey to London by granting visas to her family. The Guardian initially highlighted her case in June.

A Foreign Office spokesperson said: "We've been clear that financial sanctions against Iran are not intended to affect humanitarian goods and payments. That's why the UK argued for and secured specific exemptions to allow humanitarian transactions to take place."

The spokesperson added: "Whilst it is true that sanctions are having an impact on the Iranian population, this is compounded by the Iranian government's economic mismanagement. Iran's leaders are responsible for any impact on their people and can make the choices which would bring sanctions to an end."

Western sanctions targeting sectors from banking to trade and energy are aimed at forcing Iran's leaders to comply with their international obligations on nuclear activities.

Tehran's leaders have remained defiant against six UN security council resolutions calling on them to halt enrichment of uranium and they have refused to co-operate fully with the International Atomic Energy Agency over their nuclear programme.