Sea-Watch 3 has restarted its search and rescue mission off Libya together with the Spanish organisation Open Arms and the Italian Mediterranea.
In a statement on Friday, Sea-Watch said the ship had been unlawfully detained in Malta for almost four months, while the death rate in the Mediterranean rose to a record high.
It was let go by the authorities last month.
The fleet of three ships from three countries, which is also supported by the Moonbird reconnaissance aircraft, views itself as a civil society response to the "European Union's isolation policy" and would carry out a joint search and rescue operation in the central Mediterranean and document human rights violations.
"The EU states are haggling over the distribution of single rescued persons, while the death rate in the central Mediterranean rose to a record high in September.
"We are setting a good example and give a European response to the state-imposed state of emergency in the Mediterranean, which is committed to the ideals of solidarity and human rights," head of operations on the Sea-Watch 3 Johannes Bayer said.
He said that while arrivals dropped significantly in recent months, according to a report by the Italian Institute for International Political Studies, one in five people drowned in September in an attempt to flee across the central Mediterranean.
This figure, he said, was directly linked to the impediment of civilian rescue workers and the transfer of European responsibility to the Libyan Coast Guard.
"In view of the declining number of arrivals, the issue is not whether Europe can cope with the numbers, but whether Europe can still muster enough humanity to simply prevent people from drowning."
In a joint appeal, the organisations condemned the European Union's funding of third countries - including dictatorships and militias - to prevent refugees and migrants from entering Europe, as well as the associated violations of human and fundamental rights and of the International Convention for the Safety of Life at Sea.
They also strongly rejected the growing criminalisation campaign against migrants and refugees, which they said had developed into a governmental and judicial strategy that made the defence of humanity and solidarity a criminal offence.
Mr Bayer said: "We do not want to live in a Europe that has turned its maritime border into a mass grave as a deterrent and has its Libyan bouncers do the dirty work. We see ourselves as part of an alliance for a humane Europe at sea, on land and in the air, a Europe of safe havens and cities and communities based on solidarity. As long as the EU lets people drown in the Mediterranean, we will continue to go to sea."