Saikawa said he could not reveal all details of what had happened because the case was still under investigation.
But the company accused Ghosn of having under-reported compensation amounts, misrepresented the company's investments and used company assets for personal use.
It also accused representative director Greg Kelly of having masterminded the fraud with Ghosn. The company dismissed Ghosn and Kelly on Thursday.
As someone who had devoted himself to the Nissan revival plan, "I am left with great resentment and dismay that is difficult to articulate", wrote Saikawa.
"I truly regret, and would like to apologise for, us betraying and completely letting down our customers, business partners and other stakeholders who supported us after our revival," he wrote.
The internal memo invited all staff to a "town hall" meeting Monday with Saikawa to discuss the future of the company.
Nissan's former chairman Ghosn has since Monday been held in custody in Japan accused of having understated his income by some five billion yen (USD 44 million) between June 2011 and June 2015.
Japanese prosecutors have also accused Kelly of having a role in the offences.
Deputy chief prosecutor Shin Kukimoto said the Ghosn case was "one of the most serious types of crime" under Japan's Financial Instruments Act, and that Ghosn could face up to 10 years in jail.
The board of Mitsubishi Motors was reportedly set to meet on Monday to discuss Ghosn's future.
Renault's board has so far stood by Ghosn -- naming his deputy Thierry Bollore to handle day-to-day business.