Prosecutors said the 65-year-old had been detained over suspicions he caused Nissan $5m (£3.8m) in losses, according to reports.
In a statement, Mr Ghosn said his re-arrest was "outrageous and arbitrary".
Mr Ghosn's lawyer told a news conference they would strongly appeal against the latest arrest.
Junichiro Hironaka also said that Tokyo prosecutors had confiscated the passport and mobile phone of Carlos Ghosn's wife, Reuters reported.
Mr Ghosn, who denies any wrongdoing, was recently released on bail after 108 days in custody.
Tokyo prosecutors entered Mr Ghosn's residence before 06:00 local time on Thursday (21:00 GMT Wednesday) and took him to their office on suspicion he had misappropriated Nissan funds for personal use, Japanese broadcaster NHK reported.
Mr Ghosn's lawyer said it was almost unheard of to arrest someone after being released on bail.
"I am innocent of the groundless charges and accusations against me," Mr Ghosn said in a statement released by his representatives.
He said the arrest was "part of another attempt by some individuals at Nissan to silence me by misleading the prosecutors".