A Sudanese man was shot dead just hours after the Libyan Coast Guard returned him to shore, the UN's migration body said.
UN staffers witnessed the event which occurred in Tripoli on Thursday after 103 migrants had been returned to shore by the Libyan Coast Guard.
International Organization for Migration (IOM) staff who were present to provide aid reported to the UN body that armed men began shooting in the air when migrants tried to run away from their guards.
Many of the migrants were resisting being sent back to Libyan detention centres.
“This was tragedy waiting to happen," said IOM spokesperson Leonard Doyle in a statement. "The use of live bullets against unarmed vulnerable civilians, men, women and children alike, is unacceptable under any circumstances and raises alarms over the safety of migrants and humanitarian staff."
The event comes just two months after 53 migrants were killed after an airstrike hit a migrant detention centre outside of Tripoli.
Charlie Yaxley, the UN refugee agency's spokesman for Africa and the Mediterranean/Libya, said the incident made it "irrefutably clear that refugees and migrants must not be returned to Libya after being rescued at sea."
IOM estimates that roughly 5,000 migrants are detained in inhumane conditions in Libya with over 3,000 detained in areas of active combat.
"The migrant was struck by a bullet in the stomach. Despite immediately receiving medical aid on the spot by an IOM doctor and then being transferred to a nearby clinic, he died two hours after admission," Safa Msehli, an IOM spokeswoman said at a UN briefing in Geneva on the incident.
UN bodies and non-profit organisations have decried the inhumane conditions for migrants in Libya, where active conflict and instability persist.
Many have also criticised European countries for blocking migrants from disembarking in ports after crossing the Mediterranean and for aiding Libyan authorities despite their use of detention centres.