"We now have a totally different case, and we are only doing what we think is right", Shin Kukimoto, deputy chief prosecutor at the Tokyo District Prosecutor's Office, told reporters.
The allegations in the most recent arrest cover three money transfers from 2015 until a year ago, according to the prosecutors.
Ghosn's French lawyer has denied the allegations.
This was the fourth time Ghosn has been arrested over alleged financial misconduct.
"My arrest this morning is outrageous and arbitrary", Ghosn said according to the source via a spokesperson. I am innocent of the groundless charges and. Ghosn had been free on bail, and detaining him once again marks an unusual development in the case. He was released on bail a month earlier.
He had tweeted he would hold a news conference April 11, where he would tell "the truth" on what was unfolding.
In a statement Ghosn strongly declared his innocence.
He added his client had expected prosecutors would re-arrest him and had therefore prepared a video, without specifying the contents or exactly when it would be released.
Nissan declined to officially comment on Ghosn's new arrest.
Prosecutors deemed the new allegations completely different, necessitating a fresh charge.
Japanese prosecutors said Ghosn had been detained over transfers of Nissan funds totalling United States dollars 15 million between late 2015 and the middle of 2018.
Representatives for Ghosn could not be reached for comment about the tweet.
SBA's owner is a long-time acquaintance of Ghosn.
Prosecutors did not identify the companies involved. Renault has reported the transactions to the French prosecutor's office on suspicion the money may have been used by Ghosn for personal reasons, they said.
Such dealer incentives were not directed by Ghosn and the funds were not used to pay any personal debt, the spokesman said. Carlos Ghosn has been widely regarded as one of most influential and powerful people in the global auto industry.
He also quit as a board member of Renault-Nissan B.V., a joint venture overseeing the Japanese-Franco group in the Netherlands. Both Nissan and Mitsubishi removed him as chairman after his arrest past year.
In an extraordinary move, Tokyo prosecutors rearrested former Nissan Motor Co.
The case of Ghosn, widely credited with saving Nissan from the brink of bankruptcy, has been a rollercoaster ride of unexpected twists and turns from the moment he was first arrested at a Tokyo airport out of the blue on November 19.
That Nissan investigation that found Ghosn approved payments of around $35 million from Nissan to a distributor in Oman between 2011-18. He was out on bail since early March after spending 108 days in judicial custody.
- switching a personal currency swap contract with Tokyo-based Shinsei Bank that had an appraisal loss of 1.85 billion yen to Nissan.
The board of carmaker Renault is meeting to settle ex-chairman and CEO Carlos Ghosn's final paycheck - and wrap up its investigation into possible financial wrongdoing under his leadership.