Anonymous calls to Greek media had warned of the attack near one of the capital's busiest highways.
There were no reports of injuries or damage in the area, which is adjacent to hotels, restaurants and tourist rental sites. The Hellenic Train building also appeared to be intact.
Greek daily Efsin and news website Zugla, which received the call, said the explosive device was apparently placed in a padlocked backpack placed on a scooter without license plates.
They said the police bomb squad arrived too late to detonate the device before it exploded.
The attack was similar to one carried out outside the Greek labour ministry in February 2024.
57 people, most of them young students, died in February 2023 when a passenger and freight train collided in Tempe, central Greece, after they were allowed to run on the same track. The incident sparked widespread strikes and hundreds of protests in Greece and abroad that year.
It also led to two votes of no confidence last year and in March, which the conservative government overcame
The Italian train operator, Hellenic Train, denies any knowledge of any illegal cargo on the freight train.
More than 40 people have been held to account, including the local station manager who was in charge of the train's route. A trial for the incident is not expected to take place before the end of the year.
Intercity trains in Greece went under private management in 2017 when state-owned Greek rail operator TrainOSE was privatised and sold to Italy's Ferrovie dello Stato Italiane, becoming Hellenic Train. The Greek state-owned company OSE still owns the tracks.
Former Hellenic Train chief executive Maurizio Capotorto has reportedly been summoned to give evidence to a magistrate on suspicion of giving false testimony to a parliamentary committee about last January's crash. | BGNES