At least 29 migrants have died of hypothermia on board Italian coastguard vessels after being picked up from an inflatable boat adrift near Libya, the chief health official on the island of Lampedusa has said.

Two patrol boats picked up 105 migrants late on Sunday from the boat drifting in extreme sea conditions, with waves as high as eight metres (26 feet) and temperatures just a few degrees above zero, the coastguard said in a statement.

The migrants then spent about 18 hours on the decks of the small patrol boats taking them to Lampedusa, buffeted by high winds and spray. At least 29 died en route, Lampedusa’s mayor, Giusi Nicolini, said.

The number of dead may still rise, she said. One migrant had been taken by helicopter to the island of Sicily in critical condition, and the second patrol boat has yet to reach port.

Nicolini blamed the closure of Italy’s search-and-rescue mission, known as Mare Nostrum, last year for the tragedy. Since then no navy ships capable of keeping large numbers of migrants below deck have patrolled the waters near the Libyan coast.

“Mare Nostrum was an emergency solution to a humanitarian crisis, so closing it was a huge and intolerable step backward,” Nicolini said. Human rights groups repeatedly warned that ending the mission would endanger lives.

“The small patrol boats were completely swallowed by the waves during the trip back. If Mare Nostrum were still going, the migrants would have been given shelter inside a large ship within an hour.”

The patrol boats sent from Lampedusa are small vessels that ride low to the water so crew members can pull people in. But they cannot accommodate many below deck.

Mare Nostrum was abandoned partly because of public concern about the €114m (£85m) cost of the mission in its first year.

The EU now runs a border control operation, called Triton, with fewer ships and a much smaller area of operation.

Civil war in Syria and anarchy in Libya swelled the number of people crossing the Mediterranean last year. Many paid smugglers $1,000-$2,000 to travel.

The UN refugee agency says 160,000 seaborne migrants arrived in Italy by November 2014 and a further 40,000 in Greece. Thousands have died attempting the journey.

“To organised crime it’s not important if people make it across the sea alive or dead,” Nicolini said. “But now, without Mare Nostrum, it’s as if no one, and not just the criminals, cares if they live or die.”