Up to 700 migrants from Pakistan, Syria and Egypt were on board the overcrowded Adriana fishing trawler that set off from Libya bound for Italy. It sank off the coast of Pylos, in southwestern Greece, on June 14, 2023.
More than 100 survivors were rescued and 82 bodies were recovered.
The United Nations says about 500 more people on board perished in one of the deadliest boat accidents in the Mediterranean.
The nine defendants were on board the Adriana and charged with migrant smuggling, causing a shipwreck and participating in a criminal organisation.
But many survivors say a disastrous attempt by the Greek coastguard to tow the boat caused it to capsize in some of the deepest waters in the Mediterranean. Human rights groups and the defendants' lawyers have questioned the integrity of the Greek investigation.
The causes of the shipwreck remain a source of dispute.
Police clashed with protesters outside court in Kalamata as the migrant shipwreck trial began. (AP PHOTO)
Greece's coast guard has denied any role in the sinking and said those on the vessel had refused assistance.
It did not immediately respond to a request for comment on Tuesday.
The nine men were arrested hours after the boat sank and had remained in pre-trial detention.
They have denied any wrongdoing and their lawyers said they were being used as scapegoats.
"This is a great victory for human rights in Greece," Spyros Pantazis, one of their lawyers, told Reuters.
"Nine innocent men are walking free. Finally, after a huge struggle and pain, justice has been served."
The courtroom in the city of Kalamata erupted in applause after the judge announced the decision on Tuesday.
The men, aged from 21 to 41, hugged relatives or knelt and kissed the floor.
They all have pending asylum applications for Greece.
Before the hearing, protesters in support of the defendants briefly scuffled with police who had cordoned off the area.
"This crime will not be forgotten," protesters chanted.
"We will become the voices of the dead."
Defence lawyers said the men were charged after a rushed investigation and on insufficient evidence.
While the boat was in international waters it was sailing in Greece's demarcated rescue area.
Before the trial, lawyers accused the coastguard of monitoring the vessel for hours before launching a rescue operation and that the coastguard tried to pull the boat into Italian waters.
The coastguard has denied the accusations and has said passengers on the boat refused help.
