Senior managers at Farmal bribed a network of doctors and pharmacists to prescribe the company’s products, officials said.
They have been charged with bribery, abuse of power and corruption.
Local media said the indictment was the biggest of its kind in Croatia’s judicial history.
Correspondents say the health system could have collapsed if all the doctors implicated were sacked. There are around 5,000 doctors in Croatia.
Many of those charged were given probation fines as a result, local media reported.
In a statement, Croatia’s anti-corruption agency Uskok said the top management of Farmal, based in the northern town of Ludbreg, was charged with bribing “medical workers”, mostly primary care doctors and pharmacists, to “order and prescribe drugs produced” by the company.
“The charges are brought up against 364 Croatian citizens and Farmal pharmaceutical company for bribery, abuse of power and corruption,” it said.
The agency did not specify how many doctors have been charged, but local media reported that some 300 doctors have been indicted, according to AFP.
The suspects face up to five years’ imprisonment if convicted, the news agency said.
Doctors and pharmacists were offered bribes, including money and travel, worth between 5-10% of the medicines they prescribed, according to Sofia News Agency.
The crimes allegedly took place between 2009 and 2012.
The date for the trial has yet to be set.
Croatia has previously struggled with a widespread corruption problem but became a member of the EU in July after introducing a series of reforms.
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