He also defended the decision to transfer vigilance officer Sanjiv Chaturvedi, who had unearthed a string of corruption cases at AIIMS.
Mr Chaturvedi was shifted because his post of Chief Vigilance Officer was "opposed" by the Central Vigilance Commission or CVC, said the minister.
"The re-profiling of Mr Sanjeev Chaturvedi, the Deputy Secretary posted at AIIMS with the powers of a Chief Vigilance Officer, has generated a storm in some quarters. To the Minister what was moot was the anomaly in the very posting of a CVO without the sanction of the Central Vigilance Commission and preserving the sanctity of the institution," Mr Vardhan said in a statement. (Central Vigilance Commission Rejected Chaturvedi's Name Twice: Harsh Vardhan)
But there is no record of rejection or opposition by the CVC, sources in the health ministry told NDTV.
Mr Vardhan has himself acknowledged Mr Chaturvedi as the CVO when he acted on a case forwarded to him from the vigilance department in June this year.
In his statement, the minister claimed, "There are many aspects to corruption in hospitals which as a medico I know exist".
"I had stated on my first day in office that I will impose 500 percent transparency and adopt zero tolerance for corruption", said Mr Vardhan, adding that all systems in India's central hospitals have been placed under critical review to end "systemic and symptomatic" corruption.
The results of his efforts to end corruption, said Mr Vardhan, "would soon be in the public domain".
AIIMS Anti-Corruption Officer Shunted by Government, Doctors Question DecisionThe anti-corruption officer at AIIMS, Sanjiv Chaturvedi, who was shunted out by the government for doing his job has got support from his colleagues at the renowned institute.
A memorandum, signed by doctors at the premier hospital states that the officer proved to be "too hot to handle" for the health minister and was thus shown the door. It also says there is more to the government decision than meets the eye and that the real danger is the "manner of removal".
Speaking to NDTV, Dr Chandrashekhar Yadav, Professor at the Orthopedic department, said, "I do not feel his selection was wrong. I've seen during his tenure, patient care has gone up. He's removed so many dishonest (officials) and corrected anomalies in AIIMS. I've never seen this in my 17 years here."
The Health Minister has given two reasons for Mr Chaturvedi's removal as Chief Vigilance Officer (CVC) saying he wasn't eligible for the post and that prior approval was not taken from the CVC before his appointment.
But when we checked the rulebook we found that a deputy secretary rank officer, a position Sanjiv Chaturvedi holds, is eligible for the post of Chief Vigilance Officer (CVO) and that AIIMS is not among the 100 organisations that need prior clearance for appointing a CVO.
But the government seems to be sticking to its stand. In a tweet, Dr Harsh Vardhan defended his decision. "Sanjeev Chaturvedi twice rejected by CVC.His continuation as CVO irregular and indefensible.CVC's unattended concerns addressed at last," he wrote on the micro blogging site.
Even though the government is relying on technicalities for his removal, the move has much larger implications. It would jeopardise all the graft and corruption cases that he initiated in his two years at AIIMS and they could end up becoming null and void.
That includes cases against those who went on unexplained, illegal foreign trips on tax payers' money and the officer who got his pet dog operated on at the AIIMS cancer centre.