David Epstein, the head of the firm's pharmaceutical division, told a news briefing in Tokyo that the senior managers "resigned, they are out of the company", adding that "this kind of behaviour is unacceptable and a clear violation of our code of conduct".
"I'd like to once again apologise for Novartis' involvement in this issue," Epstein told reporters on Thursday.
The move comes after a panel of outside lawyers hired by the company said earlier on Thursday that sales staff at the scandal-hit unit also hid their improper involvement in the drug studies which were probing possible side effects of cancer treatments.
The claims marked another blow for the drugmaker, less than two months after Japanese prosecutors raided its Tokyo office over claims Novartis exaggerated the benefits of a popular blood-pressure drug.
In the latest case, the panel found that staff had removed evidence from the Novartis office of their links to the research, which pointed to at least two cases of severe reactions in patients undergoing leukaemia drugs testing.
The company hired the outside lawyers to conduct an in-house probe after allegations surfaced in press reports earlier this year about employees being involved in the testing procedure of potential side effects, which should be led by doctors only.
On Thursday, the firm said Briton Michael Ferris would replace Hiroko Ishikawa as president of Novartis Holdings Japan, while German Dirk Kosche would replace Yoshiyasu Ninomiya as head of Novartis Pharma, also part of the global firm's Japanese business.
Canadian Francis Bouchard is to succeed Kazuo Asakawa as director of the Pharma division's oncology business.
Comment: Just another example of drug company duplicity in the falsification of data to boost profits. The drive for profits overrides all other considerations, unless they are caught, in which case a sacrificial offering of a few staff is made to appease the public, along with protestations of corporate innocence.