The explosion, which caused material damage, was preceded by an anonymous telephone call to the Greek daily Efimerida ton Syntakton about an impending blast, the police said, according to AFP.
The caller warned that an explosive device had been placed in front of the ministry which would be detonated 40 minutes later.
According to media reports, the man claimed to be a member of Revolutionary Class Self-Defence, a previously unknown organisation.
The area around the building was cordoned off by the police and the device exploded at 01:29 am (2329 GMT).
Public broadcaster ERT said the device had been placed in a bag left outside the gates of a bank near the ministry.
Attacks on public establishments, banks and diplomatic representations have been recurrent in Greece for years. They are generally attributed to extreme left-wing or anarchist movements.
MNA/PR