The safety of medicines in the UK has been cast into doubt by a fraud inquiry at the European regulator responsible for licensing pharmaceutical drugs across the EU.

The European Medicines Agency, based in Canary Wharf, London, is under investigation over alleged conflicts of interest by the European Anti-Fraud Office (OLAF). If proven, the allegation would undermine confidence in the pharmaceutical industry which is already reeling from a series of disasters involving heavily publicised medicines, which later turned out to have deadly side effects.

The British multinational GlaxoSmithKline announced last week it would pay $3bn (£1.9bn) to settle US criminal and civil investigations into its sales practices, after the withdrawal of diabetes drug Avandia in 2010 due to an increased risk of heart attack.

The investigation into the European medical regulator relates to the scandal over the French diabetic drug, Mediator, which was withdrawn from the European market in 2009, a decade after initial signs that it could be responsible for fatal heart problems.

Mediator, made by French pharmaceutical firm, Servier, was on the market for 33 years and was prescribed as a weight loss drug taken by an estimated 5 million people in France and by many more in Italy and Spain. It is estimated it caused between 500 and 2,000 deaths, mainly from heart valve problems, before it was banned. Mediator was not marketed in the UK, but the fallout from the scandal has damaged confidence in the drug regulatory system.

The chief executive of the French regulator, the Health Products Safety Agency, resigned and the body which he headed was overhauled after a damning official report said it "failed in its duties." The reformed regulator, renamed National Agency for the Safety of Medicines (ANSM), includes new measures to guarantee transparency and avoid conflicts of interest.

The investigation into the EMA was triggered by Michèle Rivasi, a French Member of the European Parliament for Europe Ecologie Les Verts, a green party. She has pointed out that 80 per cent of its budget comes from the pharmaceutical industry making independent oversight impossible.

The EMA was created in 1995 to harmonise drug regulation systems in the EU. It said last month it had "strengthened the rules on how it handles potential conflicts of interest of its staff and experts" after it was criticised by the agency's Budgetry Control Committee.