The company also said it was freezing funding for clinical trials in the country in the wake of the scandal, which David Epstein, head of the firm's pharmaceutical division, branded "unacceptable and a clear violation of our code of conduct".
Epstein told a press briefing in Tokyo that the senior managers "resigned, they are out of the company".
"I'd like to once again apologise for Novartis' involvement in this issue," he said.
"If some of them have destroyed documents, it's a pure violation of our code of conduct and that employee has to leave as soon as we discover that," Epstein said.
More From This Section
The move comes after a panel of outside lawyers hired by the company said earlier Thursday that sales staff also hid their improper involvement in drug studies probing possible side effects of cancer treatments.
The claims marked a fresh 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.
The probe found sales staff had acted inappropriately by involving themselves in the clinical research at nearly two dozen medical institutions in Japan.
The panel did not find evidence that the data were falsified, but "we noted that there were several irregular practices", said a lawyer speaking on behalf of committee head Kunio Harada.
Today, Novartis also said it would freeze funding to doctor-led clinical trials in Japan until its probe concludes.
"We have to restore trust in our company," Epstein said.
"We have to put the patient first, patient confidentiality is key. Separation of commercial from development is absolutely key, shredding a document is unacceptable. Any unethical behaviour is unacceptable for a global company like Novartis," he added.
Failing to report the side effects of a drug could violate pharmaceutical law "which could mean an administrative penalty," a health ministry official told AFP.
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, which should have only been led by doctors.