Al-Madina president Adnan Abu Ayyash accuses General Rustom Ghazaleh and three brothers of spiriting away $72 million from the bank between 2000 and 2003, Abu Ayyash's lawyer Jean Azzi said on Thursday.
Ghazaleh headed the much-feared Syrian intelligence that left Lebanon last month as part of a troop withdrawal that ended Damascus's 29-year military and political grip on its smaller neighbour.
The Central Bank of Lebanon appointed an administrator to run the privately owned al-Madina in July 2004 after finding a $1.2 billion hole in its accounts, the worst financial scandal in the country in three decades.
The bank is also facing a money-laundering investigation. Unconfirmed press reports said the bank was used to launder several trillion dollars by the Russian mafia, Iraqi state funds and Saudi Islamic associations.
Abu Ayyash has also accused a former official with the bank, Rana Qoleilat, of involvement in the alleged embezzlement.
Qoleilat, who played a major role in running the bank, is under investigation for falsifying documents and embezzling tens of millions of dollars through bad cheques.
She was arrested last year but released on bail in April on the eve of the Syrian pullout from Lebanon.
Abu Ayyash's brother, Ibrahim, a co-owner of the bank, was arrested along with Qoleilat, accused of embezzlement and abuse of trust and is being detained in jail.