Ostojic said he was briefed about the operation dubbed "Hippocrates" by State Prosecutor Mladen Bajic.
The minister said the health care system in Croatia was not in jeopardy because of the operation.
He called the press conference after it was reported that the anti-corruption office USKOK had taken into custody the head of the Farmal pharmaceutical company and physicians suspected of receiving bribes from pharmacists to prescribe their drugs.
Ostojic said he could not say more about the operation because it was an USKOK case, but added that "this is a good day for our society because combating corruption is a national interest."
"In the last few years, corruption has become socially acceptable behaviour, which is intolerable. I won't tolerate any form of corruption in health care. People like this cause enormous damage to the profession, but also to patients."
Ostojic said a lot had been done in health care, private monopoly has been abolished, public money no longer ending up in private pockets, and public procurement has been combined.
Croatia has 5,000 primary care physicians and "corruption is a personal feature, certainly not a professional one," he added.
"Corruption is widespread, so we should support such operations. Believe me, there will come a time when we will have a society without corruption," Ostojic said, adding that the Health Ministry had saved HRK 100 million (appeox. 13.3 million euros) by not buying outdated medical equipment.
Croatian Physicians' Chamber president Hrvoje Minigo supported anti-corruption operations in health care and regretted "such cases."
Speaking to Hina, he said corruption was not in the code of the medical profession and that the Chamber would be able to launch disciplinary procedures against the physicians involved in this case only after they were sentenced.
The Croatian Health Insurance Institute (HZZO) also supported the "Hippocrates" operation, saying in a statement that uncovering abuse among health care workers served to protect insurees and the money they set aside for health care.
In light of announcements that family doctors will be criminally charged, the HZZO will make sure that no insuree is left without primary care, the statement said.