Kos is dealing with the aftermath of an earthquake that killed two people and injured hundreds on the Greek holiday island.

The 6.7-magnitude quake left hundreds more injured in the Turkish resort of Bodrum, about 12 miles (20km) across the sea from Kos. Tourists have faced flight delays and the damaged main harbour was closed for a second day.

“Given the amount of people outside at the time, having only two victims is a miracle,” said the deputy Kos mayor, David Yerasklis.

The undersea quake struck at 1.31am on Friday between Kos and Bodrum, when many tourists in both places had been out enjoying the nightlife.

On Kos, a wall collapsed on people in the courtyard of a nightclub, killing a 22-year-old Swedish man and a 39-year-old Turk.

Another 120 people were hurt, seven of them seriously, while some 360 people were injured in Bodrum, many after jumping out of windows.

The badly injured on Kos were flown to hospitals in Athens and Crete, including two men from Sweden and Norway who were in critical condition. Medics said the Swede lost his lower leg, and doctors are struggling to save his other leg. The Norwegian has serious head injuries.

Kos is one of Greece’s top travel destinations, particularly popular with British, German and Scandinavian tourists. The quake struck at the height of the tourism season.

The Greek prime minister, Alexis Tsipras, warned against “dramatising” the issue. “Creating a climate of exaggeration and dramatisation does not help restoring normality in daily life on the island,” Tsipras’s office said.

A boy stands next to a car crushed under rubble on Kos. Photograph: AFP Contributor/Getty Images

Government officials and expert divers on Saturday were inspecting Kos’s harbour, the floor of which was cracked by the tremor and has been declared unsafe for use. But the rest of island’s infrastructure network including roads is mostly intact, they said.

Ferries have been rerouted to the smaller port town of Kefalos in west Kos until repairs are made. “All scheduled ferry services are now running from Kefalos, both incoming and outgoing,” a coastguard operator said.

Many people spent the night outdoors as a precaution, setting up tents in parks and squares, but officials noted that the majority of hotels were unaffected by the quake.

Deborah Kinnear, 35, a psychologist from Glasgow, said her family initially thought of returning home but no flights were available.

“I think calm is being restored,” she said after spending the night outdoors. “Last night wasn’t too bad. Hoping the worst is over ... this has been one of our best holidays.’

At Kos airport delays continued for a second day with more than 50 outgoing flights scheduled. About 20 flights had landed by midday on Saturday.

“There is no problem at the hotels, the tourists have dealt calmly with developments,” said Constantina Svynou, the head of the local hotelier association.

Workers remove rubble from a quake-damaged mosque in Kos. Photograph: Louisa Gouliamaki/AFP/Getty Images

Some areas of the port town were still without water. No injuries were reported among the 800 migrants and refugees housed on the island, which is one of the main gateways into Europe for people fleeing war and poverty. Asylum procedures have been curtailed until at least Monday as the quake damaged passport inspection facilities at the harbour.

Many archaeological and medieval monuments, including the medieval Knights of St John fortifications near where the deaths occurred, have also been closed. The earthquake toppled the minaret of an 18th-century mosque and knocked boulders off the fortifications.

Turkey and Greece sit on significant fault lines and are regularly hit by earthquakes. This year, Turkey’s western Aegean coast has been affected by several significant tremors.

In June, a 6.3-magnitude earthquake gutted a village on the Greek island of Lesbos, killing a woman and leaving more than 15 injured.