Six coastguard officers were lowered from a helicopter onto the deck of the Ezadeen as it floated some 40 kilometres off Crotone on Italy's heel, the navy said.
It marked the second such drama in days for Italy, which is struggling with a record wave of migrants making the perilous journey across the Mediterranean, after the navy on Wednesday stopped another crewless "ghost" ship with hundreds of migrants on board.
A shipping website, however, said the Sierra Leone-registered vessel had begun its voyage in the Syrian port of Tartus. Thousands of the refugees who have ended up in Italy this year had fled the war-torn country, but most have come via North Africa.
Prior to apparently running of fuel, the almost 50-year-old ship had been moving at a brisk seven knots and had been spotted by a coastguard plane 80 miles offshore shortly after nightfall.
"We are alone, they is no one, help us!" she cried, he said.
The coastguard asked for assistance from Icelandic patrol boat Tyr, which was in the area on a mission with Frontex, the European Union's border agency.
The Tyr was able to draw alongside the runaway ship, but the weather conditions made boarding impossible.
The Icelandic vessel has three doctors on board who are waiting to be winched on to the merchant ship by helicopter to treat any unwell passengers, the air force said.
