Sea-Watch said another 15 migrants are missing after the attackers boarded the boat and beat them with clubs, throwing many into the sea.
The group claimed that the speedboat carrying the armed men was marked `Libyan Coast Guard`.
Around 150 migrants were crammed on board the boat.
"The violent intervention of the Libyan Coast Guard caused a situation of mass panic on board the rubber boat in distress," Sea Watch said in a statement.
"One tube of the rubber boat collapsed, causing the majority of the 150 people to slip into the water."
The group said it had launched a rescue operation following the incident, which happened overnight on Thursday.
A spokesman for Libya`s naval forces in Tripoli said he had not heard of the attack.
Boat loads of migrants regularly attempt the dangerous journey across the Mediterranean.
The Italian coast guard, which coordinates the operations carried out by aid ships, said around 1,400 migrants were rescued on Thursday off the coast of Libya.
Attempts at the crossing are continuing despite worsening weather as winter approaches, with more than 2,400 migrants rescued off Libya since Sunday.
The medical charity Medecins Sans Frontieres tweeted that it had rescued 802 people on six rubber dinghies and one small wooden boat.
A Maltese aid group said it had rescued 432 migrants packed on to three dinghies.
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