The ship's captain and three workers are facing criminal charges over the death at the port of Piraeus in Athens.
Greece's merchant marine minister, Miltiadis Varvitsiotis, has resigned over comments he made on TV following the death of a passenger, Antonis Kargiotis, who was allegedly pushed off a ferry by crew members.
Varvitsiotis said his remarks, in which he appeared to back the ferry's crew over the incident last Tuesday, have been "misinterpreted," Barrons News reports, quoting AFP.
The ship's captain and three workers are facing criminal charges over the death at the port of Piraeus in Athens.
The incident has caused outrage in Greece.
A video posted on social media showed the 36-year-old passenger, identified as Antonis Kargiotis, running onto the Blue Horizon ferry's loading ramp as it was preparing to sail from Athens to Crete.
Crew members on the ramp appeared to try and physically stop Kargiotis from boarding. The video then shows him seemingly being pushed into the sea.
The ferry left as scheduled - only turning back when the authorities instructed it to return to port. The man's body was later retrieved from the water.
Last week, Varvitsiotis told Greek TV that "the families of those who went to earn a wage, a day's pay, and are now being accused of murder, are also mourning".
He was roundly criticised for the comments, with Greek newspaper Ekathimerini calling Varvitsiotis' statement "entirely misguided and deeply regrettable".
On Monday, Varvitsiotis in his resignation letter posted on X, formerly known as Twitter, said Kargiotis' death had "shocked us all".
"The murder of Antonis Kargiotis by members of the Blue Horizon (ferry) crew shocked us all," Varvitsiotis said in his resignation letter.
But he added he had become the target of a "toxic" attack after his statement had been "misinterpreted".
"In no way did I equate the victim with the perpetrators," he said. "I don't accept being stoned as a human being.”
Last week, Greek Prime Minister Kyriakos Mitsotakis wrote on Facebook that he felt "disgust and horror at the unimaginable end found by one of our fellow countrymen" which "the mind can't comprehend".
Mitsotakis said the death was the result of "a combination of irresponsibility and cynicism, contempt and indifference" and promised the state would do its "duty".
A government spokesman said the prime minister had accepted his resignation.
The ferry captain and three crew members appeared in front of a prosecutor on 6 September, the day after the man's death.
The captain faces felony charges of dangerous interference with maritime traffic, while the crew member who allegedly pushed the passenger faces charges of manslaughter with possible malice.
The other two crew members are being prosecuted for complicity in the manslaughter, the AFP news agency reported.