The Italian ship Vos Thalassa rescued 67 migrants, including six children, off the coast of Libya on Sunday while responding to a distress call.
But when the Italian crew turned to to meet the Libyan coast guard the migrants threatened to behead the Italian crew.
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The Italian government then intervened to rescue the crew of the rescue ship.
Italy intervened in a migrant rescue by a private Italian ship this week after migrants reacted to attempts to hand the operation over to Libyan authorities by threatening the crew, the vessel said.
The Vos Thalassa took 67 migrants, including six children, onboard on Sunday after responding to a distress call off the Libyan coast.
Several local and international media reports said the ship was denied permission to dock in Italian ports because of the migrants, marking the first time the government had turned away an Italian vessel.
The migrants were then handed over to the Italian coast guard, the reports said.
However, international shipping company Vroon, which operates Vos Thalassa, an oil rig supply vessel, told Euronews that the ship “never requested to enter an Italian port or even Italian territorial waters.”
Vroon said that when the vessel turned to meet with the Libyan coast guard to transfer the migrants, they “started to threaten the crew, surrounding and pushing them and making ‘cut your throat’ gestures.”
“Because of these threats the vessel returned to its position and reported this situation to the MRCC [Maritime Rescue Coordination Centre] in Rome.”
The shipping company said being “severely outnumbered on board a merchant vessel by an angry crowd that has very little to lose is very frightening”.
“We are very proud of the professionalism of our crew in these very challenging circumstances.”