Greece is facing a serious shortage of medicines amid claims that pharmaceutical multinationals have halted shipments to the country because of the economic crisis and concerns that the drugs will be exported by middlemen because prices are higher in other European countries.

Hundreds of drugs are in short supply and the situation is getting worse, according to the Greek drug regulator. The government has drawn up a list of more than 50 pharmaceutical companies it accuses of halting or planning to halt supplies because of low prices in the country.

More than 200 medicinal products are affected, including treatments for arthritis, hepatitis C and hypertension, cholesterol-lowering agents, antipsychotics, antibiotics, anaesthetics and immunomodulators used to treat bowel disease.

Separately, it was announced on Tuesday that the Swiss Red Cross was slashing its supply of donor blood to Greece because it had not paid its bills on time.

Chemists in Athens describe chaotic scenes with desperate customers going from pharmacy to pharmacy to look for prescription drugs that hospitals could no longer dispense.

The government list includes some of the world's leading pharmaceutical companies, such as Pfizer, Roche, Sanofi, GlaxoSmithKline and AstraZeneca. Pfizer, Roche and Sanofi all said a few products had been withheld. GSK and AstraZeneca denied the claims.

"Companies are ceasing these supplies because Greece is not profitable for them and they are worried that their products will be exported by traders to other richer countries through parallel trade as Greece has the lowest medicine prices in Europe," said Professor Yannis Tountas, the president of the Greek drug regulator, the National Organisation for Medicines.

The regulator has investigated 13 pharmaceutical companies that have reduced supplies and has handed the names of eight to the ministry of health so they can be fined. Tountas did not disclose the names of the companies, saying this was the responsibility of the ministry of health, but added that they were "big multinational companies".

The body representing pharmacists, the Panhellenic Pharmaceutical Association, confirmed the shortages. "I would say supplies are down by 90%," said Dimitris Karageorgiou, its secretary general. "The companies are ensuring that they come in dribs and drabs to avoid prosecution. Everyone is really frightened. Customers tell me they are afraid [about] losing access to medication altogether." He said many also worried insurance coverage would dry up.

"Around 300 drugs are in very short supply and they include innovative drugs, medications for cancer patients and people suffering from clinical depression," said Karageorgiou. "It's a disgrace. The government is panic-stricken and the multinationals only think about themselves and the issue of parallel trade because wholesalers can legally sell them to other European nations at a higher price."

The Hellenic Association of Pharmaceutical Companies said the picture was more nuanced. Its president, Frouzis Konstantinos, said there were "probably a very few companies" that were not supplying the Greek market, and only for very specific products — "the reasons being a combination of Greece's low medicine prices and unpaid debt by the state", he said.

In Athens and Thessaloniki, Greece's second city, chemists say they are often overwhelmed by people desperately trying to find life-saving drugs. Oscillating between fury and despair, the customers beseech pharmacists to hand over medications that they frequently do not have in stock.

"Lines will form in the early morning or late at night when you're on duty," said Karageorgiou, who is based in Thessaloniki. "And when the drugs aren't available, which is often the case, people get very aggressive. I'm on duty tonight and know there will be screaming and shouting but in the circumstances I also understand. We have reached a tragic point."

Greece's social insurance funds and hospitals owe pharmaceutical companies about €1.9bn (£1.6bn), a debt going back to 2011, with companies expecting payments of €500m this month.

Some companies admitted they were not supplying some medicines. According to the government list, Pfizer had not supplied or would not be supplying 16 medicines. A company spokesperson disagreed with the total but confirmed four medicines had been withdrawn "because alternatives were available and because of the parallel trade [reselling] situation in the country". The products are the two leukaemia treatments Zavedos and Aracytin, which were withdrawn last year, and the analgesic Neurontin and the epilepsy therapy Epanutin, which were withdrawn last month.

Roche stressed it had not halted supplies of medicines to Greece, but said it had withheld supplies to public hospitals that owed the company €200m. Daniel Grotsky, a spokesman, said: "We are insisting that they [the public hospitals] fulfil their contracts and this is something we do in any country … We are withholding [medicines] until they meet their obligations."

Roche could not say how many hospitals were affected but said it was still supplying public hospitals with "critical medicines", which included treatments for HIV and transplantation. Grotsky said patients could still get their medicines through pharmacies.

Angeliki Angeli, spokeswoman for Sanofi Greece, said it was supplying public hospitals with medicines considered life-saving, unique or irreplaceable. "Non-unique products are supplied based on hospitals' outstanding obligations and overdue status," she said. Non-unique products are medicines for which either a generic exists or a therapeutic alternative option is recommended by treatment guidelines.

She said most Sanofi medicines on the government list remained available on the market with the "exception of a couple of dosages/forms where alternatives exist".

GSK Greece said it had never halted the supply of any product in the Greek market. "This is a joint decision taken not only at local level but also at corporate level. Equally, GSK has maintained the uninterrupted supply [to] Greek public hospitals with all its products irrespective of the accumulated debts," the company said.

Vanessa Rhodes, of AstraZeneca, said the company had not halted the supply of any of its medicines to Greece. "Our priority is to ensure patients have access to the medicines they need. Furthermore, we have an emergency 'direct–to-pharmacy' supply system in place should pharmacies find themselves out of stock of any of our products."

Zeta Chatziantoniou, of Boehringer Ingelheim in Greece, stressed it "has not halted any of its medicine supplies in Greece in the retail sector and in the public sector". Novartis said it was not halting supplies to Greece.

The pharmaceutical industry says many shortages are because of products being exported through parallel trade, and has urged the government to address set drug prices. Under EU trade rules, the free movement of goods is allowed. So for example, while a pharmaceutical company may sell a medicine to a wholesaler or pharmacist in Greece, the wholesaler or pharmacist can sell these medicines on to wholesalers in other countries. Parallel traders do this to make money on the price differences between countries.

"The government needs to correct these wrong prices to avoid a surge of exportation. Greece's drug prices are 20% or more lower than the lowest prices in Europe," said Konstantinos, who is also the general manager of Novartis in Greece.

The industry wants the health ministry to bring in a new pricing system so that Greece uses a basket of eurozone countries to calculate prices. At present, medicines are priced at below the average of the three lowest prices in 22 EU countries.

The regulator has introduced export bans for nearly 60 medicines to try to tackle the problem and is looking at 300 more products. It is also investigating 10 wholesalers and 260 pharmacists who it believes have broken the export ban. The ministry of health will decide any punishment, which is likely to be fines ranging from €2,000 to €20,000, said Tountas.

This month will be crucial as Greek officials and Greece's creditors – the European commission, the International Monetary Fund and the European Central Bank – must agree the 2013 public pharmaceutical budget, which has fallen in recent years. More cuts would put patients at a "critical level", said Tountas, who will be one of the key players at the negotiating table. The budget was €3.7bn in 2011 and fell to €2.44bn last year. Tountas is concerned creditors may cut it to €2bn for 2013.