Norihisa Tamura on Friday characterized as "extremely regrettable" an incident in which an employee of the world's number two drug maker had hidden his affiliation during a medical study into the effects of Valsartan.
A study at Kyoto Prefectural University of Medicine concluded that the drug, developed to treat high blood pressure, could also help to prevent strokes and angina.
But the university said on Thursday that incomplete clinical data had been used to support this finding and that had patients' records been used in their entirety, the study would have had a different conclusion.
While Valsartan was effective in controlling high blood pressure, the university said the medication did not necessarily have any effect on strokes or angina.
Novartis sells the drug under the name "Diovan" in Japan, where it is one of the most commonly prescribed drugs on the market.
It is licensed for use in more than 100 countries.
The firm used the study to market its drug, playing up its supposed additional benefits.
Tamura said the case "highly suggests fabrication and falsification of data" and he would be establishing a special committee to work out how to prevent this in future studies and to review ethical guidelines.
The study was led by professor Hiroaki Matsubara, and included among its researchers an un-named Novartis employee, who was identified as an adjunct lecturer at Osaka City University.
Matsubara resigned his post at the university in February after scientific journals pulled his papers citing inconsistent data and as the school launched a probe.
The Novartis worker, who has already left the firm, has refused to cooperate with the university's investigation.
In a statement issued on Friday, Novartis maintained that the university was unable to conclude that there was intentional wrong-doing.
The Basel-based company said the inconsistencies might be unintentional errors, not the "manipulation" suggested by the university.
The Novartis researcher was also involved in Diovan research at Tokyo Jikei University, Chiba University, Nagoya University and the Shiga University of Medical Science, Kyodo News said.
These universities have said they will also conduct investigations to see if there were any problems.