After a long tug-of-war with Malta, which had taken over the coordination of the rescue without sending ships and denying availability to receive migrants on the island, the Italian government brought in the Guardia di Finanza and Coast Guard vessels to escort the fishing boat.
Italy's far-right Interior Minister Matteo Salvini earlier urged Malta to rescue some 450 migrants on board a large boat that at the time was in Malta's search-and-rescue area, saying "this boat can not and must not arrive" in Italy.
Italy's new populist government, which includes the anti-migrants League party, is leading a crusade against migrant arrivals and foreign ships that rescue them in the Mediterranean.
The migrants were saved by two ships, one operated by European Union border agency Frontex and one owned by Italy's tax police.
Police check a migrant who has now left the Frontex ship "Protector" at the port of Pozzallo.
But the two patrol vessels remain stranded in Italian waters with both Italy and Malta not allowing them to dock.
According to Italian media, sailors aboard the Vos Thalassa locked themselves in the control room and called for help after two migrants with mobile phones and Global Positioning System realised that the boat was heading south back towards Libya, sparking a furious reaction from some on board.
According to a map of the migrant boat's position provided buy Malta, it is now between Lampedusa and Linosa, both Italian islands and more than 100 nautical miles from Malta.
They were transferred to Italy's coast guard vessel after two migrants allegedly launched threats against the freighter's crew if the ship was sailed back to Libya, according to state-run RAI News TV channel.
The 67 were eventually allowed to disembark late on Thursday evening after and intervention by the Italian President Sergio Mattarella.
Since taking office last month, Salvini has led a high-profile campaign to shut humanitarian rescue ships out of Italy's ports, which means there are now no charity ships to help out with rescues. Mr. Salvini has promised to keep his promise and not give in to pressure tactics.
"I have to do everything I can to protect the people who live in this country", Salvini said on RTL radio on Friday.
The ministry claims that Malta took charge of the operation and asked Italy for "naval help" while not sending any of its own vessels "capable of providing assistance" to the area.
Spokesman Kurt Farrugia said on Twitter that when Valletta was notified of the ship's presence it was 110 nautical miles from Malta and 53 nautical miles from Lampedusa. Italy's transport minister said Malta must let the ship dock.
The 67 migrants - including three women and six children - were earlier held at the port in Trapani as a row brewed over reports that a handful of the group revolted after they were rescued, amid fears that they would be returned to Libya.