IERAPETRA, Greece -- Hour after hour, the coast guard boats shuttled from the crippled freighter to a concrete pier, discharging a steady flow of humanity: Families with small children, black-clad elderly women, battered-looking youths with backpacks.

For more than 700 migrants, most of them fleeing the conflict in Syria for Europe, the harrowing journey on a smuggling ship that broke down in gale-force winds ended Thursday in the southern town of Ierapetra on the Greek island of Crete.

The Baris cargo ship lost engine power Tuesday in international waters, and limped into Ierapetra at sunrise after being slowly towed for 40 hours by a Greek navy frigate.

Authorities said its passengers were exhausted but overall in good health.

In brief interviews while being shepherded away by police, many said they had fled violence by militants from the Islamic State group in Syria or Iraq.

"They attacked us and killed our people, so we came here to save ourselves," said one man who said he was from Iraq. He only identified himself by his first name, Mohaned, to protect his kin, who stayed behind, from retribution.

Another who identified himself as Qassim, from the besieged northern Syrian town of Kobani, said he and his family had spent 11 days on the Baris.

As dozens of Ierapetra residents looked on from behind a police cordon, newly-disembarked passengers received preliminary care and food before being taken to temporary shelter at a basketball arena. One young woman knelt and kissed the rough harbour concrete, and a child held a piece of cardboard that read: "Thanks for Greece government saving children in the ship."

It was one of the largest single crossings of its kind in recent years. Tens of thousands of people fleeing war and poverty in African and the Middle East risk the journey to Europe every year, paying smuggling gangs to transport them in usually unseaworthy craft ranging from dinghies to aging rust-buckets. Most end up in Italy.

According to Greek security and health officials, about 500 of the migrants said they were Syrians. One official involved in the operation said the passengers had been charged $2,000 to $6,000 to be taken to Italy, and about 20 suspected smugglers were arrested on the ship. He asked not to be named as he was not authorized to brief the press.

According to the latest figures from the U.N. refugee agency, UNHCR, at least 3,000 people have drowned or disappeared trying to make the trip this year -- almost 2 per cent of the estimated total of 165,000 to attempt the journey.

The 77-meter (250-foot) cargo ship lost power the same day Pope Francis called on European governments to do a better job of welcoming migrants in speeches to the European Parliament and Council of Europe. Francis said "we cannot allow the Mediterranean to become a vast cemetery!"

The mayor of Ierapetra, a town of 16,000 people on a wide, open bay overlooked by jagged hills, said he sympathized with the migrants. But stretched local authorities couldn't offer them shelter indefinitely, Theodossis Kaladzakis said.

"Ierapetra can look after these people for a week, but afterward, unfortunately, we simply won't have that ability," he said. "It's not that we don't want to. We just can't."

Doctors conducted preliminary health checks and polio vaccinations for children from Syria, where the disease has made a comeback, senior Greek public health official Panayiotis Efstathiou said. Kurds, Afghans and Palestinians were also aboard the ship, which originated in Antalya, Turkey, Efstathiou told The Associated Press.

A pregnant woman, who was hemorrhaging, was airlifted to a hospital Wednesday, but there were otherwise no reports of serious health problems aboard the Baris. Rumours of armed men aboard the vessel proved unfounded, the coast guard said.

Efstathiou said the Syrians will receive refugee status and be released, while other passengers deemed to be in Greece illegally will be interned pending deportation.

A UNHCR spokeswoman in Athens said more than 99 per cent of Syrians reaching Greece eventually gain refugee status in a lengthy and cumbersome process.

"There are people who have to visit application centres, which can handle very few people a day, 10-15 times," Ketty Kehagioglou said. "And there should be a mechanism for their integration, because now people complete the refugee process and then end up in the street."

Bishr El-touni contributed to this story.