Government lawmakers approved the probe into the actions of Kostas Karamanlis, who has welcomed the investigation as an opportunity to clear his name.
The tragedy sparked sweeping strikes and hundreds of protests in Greece and abroad.
He insisted he had done “everything” in his power to improve the state of Greek railways.
“I too want justice... I fully support the proposal” to set up a special inquiry committee, he added.
Opposition parties, who had sought criminal charges for Karamanlis, accused the conservative government of seeking to “launder” its responsibilities by backing a probe into a lesser charge.
Taking the floor on Wednesday, Mitsotakis dismissed as “disgraceful” a proposal by leftist and far-right parties to have him investigated for high treason.
Lawmakers already voted to refer a former junior minister, Christos Triantopoulos, to justice on possible misdemeanour charges for breach of duty in connection with the aftermath of the accident.
Triantopoulos denies wrongdoing.
In April, a bomb exploded outside Hellenic Train’s offices, without causing any injuries.
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