"I am sorry to investors, customers and of course our workers", said Saikawa.
Board member Yasushi Kimura told reporters at an evening news conference at company headquarters in Yokohama that the board has approved Saikawa's resignation, effective September 16, and a successor will be appointed next month.
"Today, the Board of Nissan Motor Co., Ltd. held their regular Board of Directors meeting". He has said he was unaware of the adjustment.
Asked how he felt towards his once-mentor Ghosn and Kelly, Saikawa said he believed their actions had put the company in the hard position in which it now finds itself - with hardship for customers, staff and dealers.
Saikawa said he wanted to "pass the baton" to a new generation of executives and had told colleagues he meant to step down, the Nikkei said.
Kimura and three other board members, who all have backgrounds outside the company, said their investigation of the scandal over Ghosn's arrest found that alleged misconduct by Ghosn and Greg Kelly, a former board member who was also arrested, had caused 35 billion yen ($350 million) in damage to the company.
Nissan said it had no immediate comment on the reports, which first emerged overnight.
An alliance source told Reuters that a nominations committee established in June to find a successor to Saikawa had drawn up a shortlist containing more than 10 possible candidates. Saikawa, who admitted to the overpayment last week, will be temporarily replaced by Chief Operating Officer Yasuhiro Yamauchi, with a permanent replacement expected by the end of October, the Japanese company said.
"I left the issue to someone else so I had thought it was dealt with in an appropriate manner", he told reporters, adding that he would repay the sum to Nissan.
Nissan doesn't consider the excess payment to have violated any laws, and Saikawa has denied he ordered the payments, saying the matter was mishandled by staff.
Saikawa is suspected of improperly adding 47 million yen (USD 440,000) to his compensation by altering the terms of a bonus. The former chairman is out of jail on bail and due to face trial in Tokyo next year on charges that he failed to disclose compensation from Nissan, passed on trading losses to the carmaker and redirected company money into his own accounts. He has also been charged with breach of trust for allegedly funneling company money for personal gain.
In the months since, Nissan has announced plans to slash 9% of its workforce amid falling profits.