Italianauthorities opened an investigation on Sunday into the murder of an African migrant allegedly shot by a people smuggler because the migrant refused to give up his baseball cap, police said.

The inquiry was opened as thousands of migrants arrived in Italy from Libya following a surge in smuggling activity.

The body of the 21-year-old man was unloaded in the Sicilian port of Catania on Saturday from rescue ship Phoenix, operated by the Malta-based Migrant Offshore Aid Station (Moas).

The organisation brought back 394 migrants, including another with a gunshot wound and the elder brother of the dead man who allegedly witnessed the killing aboard the smuggler’s boat for Italy.

Regina Catambrone, the founder of Moas, disclosed the murder at a news conference at which she strongly denied claims by Italian politicians and magistrates that her organisation was among organisations allegedly suspected of conniving with traffickers.

“We are seeing manipulation by political parties," she said. "We are interested in saving human lives.”

Italian officials struggled to cope with the arrival of more than 3,000 migrants who were being brought to Sicily this weekend after being rescued from the Mediterranean by the Italian Coast Guard, a Spanish Navy warship and vessels operated by charities including Save the Children.