With more than 200 people on board the Louise Michel tweets from the ship's account said it had been left "unable to move" with "Europe ignoring our emergency calls for immediate assistance".
The group has now said "all remaining guests" have now been transferred to another humanitarian ship - while dozens were helped by the Italian Coastguard.
Those associated with the Louise Michel former French navy vessel warned: “It’s not over”, as they demanded safe refuge for “survivors”.
At one point on Saturday there were 219 people on board the boat, including 33 in a life raft deployed by its side and one corpse in a body bag, someone involved in the mission said.
The vessel – launched under its new humanitarian guise last week – was left stranded off the coast of Malta for around 12 hours, according to tweets posted from the ship’s account.
One tweet said: “#LouiseMichel is unable to move, she is no longer the master of her manoeuver, due to her overcrowded deck and a liferaft deployed at her side, but above all due to Europe ignoring our emergency calls for immediate assistance. The responsible authorities remain unresponsive.”
Another read: “We repeat, #LouiseMichel is unable to safely move and nobody is coming to our aid. The people rescued have experienced extreme trauma, it’s time for them to be brought to a #PlaceOfSafety. We need immediate assistance.”
Those associated with the vessel, which features a Banksy painting depicting a young girl holding on to a heart-shaped safety float, said it could not safely move because of an overcrowded deck.
A summary of a series of calls for assistance to various authorities was also posted, but they got no answer or were told there was no assistance available, the account said.
But the Italian Coastguard stepped in to evacuate 49 of the “most vulnerable” on board on Saturday afternoon - as well as the body of a male who died before the Louise Michel could reach a rubber boat a day earlier, a tweet from the ship organisers’ account said.
Another humanitarian ship Sea-Watch 4 – a joint project between United4Rescue, Sea-Watch, and Doctors without Borders – took all the remaining people on board.