The three migrant workers fled Libya in March 2011 aboard an inflatable rubber boat just a month after the NATO military alliance established a no-fly zone as rebels battled to oust long-time dictator Moamer Kadhafi.
Veronique van der Plancke, lawyer for the three, said they were filing suit "for war crimes and failing to come to the assistance of people in danger."
Their boat left Tripoli aiming for the Italian island of Lampedusa - where refugee shipwrecks have cost hundreds of lives this year - but it broke down half way.
A statement issued by international human rights groups said the boat and its 72 refugees - including women and children - were left adrift for 15 days, with 63 dying as a result, even though they were sighted by NATO ships and aircraft.
The complaint alleges specifically that "Belgian military forces present in the area... Failed to respond, violating the obligation to assist persons in danger," the statement said.
The case "also calls into question the responsibility" of other NATO units, it said, noting that the survivors have filed similar complaints in Italy, France and Spain.
The plight of refugees, many from the Horn of Africa, was tragically highlighted in October when some 400 drowned in the Mediterranean trying to get to Italy's Lampedusa.
EU leaders pledged to do more to bring the refugee inflow under control and improve rescue coordination efforts but rights groups claim this is still not enough.
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