Italian-flagged NGO ship Mare Ionio said on Wednesday that authorities in Rome ordered it to get instructions from Libya as the boat rescued 98 migrants - including 22 young children - from a deflating dinghy in the Mediterranean.
"As always, to our requests the Italian Maritime Coordination Centre has replied that we have to deal with 'Libyan authorities'," the Mediterranea Saving Humans charity, which operates the Mario Ionio, wrote on Facebook.
"We have replied that we can't refer to the forces of a country which is stage of a civil war, where everyday the world is witnessing tortures and inhuman treatments," the post continued.
""The people we rescued are now aboard an Italian ship, the Mare Jonio, and their safety is our responsibility."
The NGO said it had emailed Italy to ask for new instructions "compatible with the international law of the sea and human rights."
Among those rescued by the Mare Ionio are at 26 women, at least 8 of whom are pregnant, 22 children under age 10 and at least 6 other minors, according to Mediterranea Saving Humans.
"Libya is not a safe country and no one should be take back there," United Nations refugee agency UNHCR spokeswoman Carlotta Sami tweeted on Tuesday.
At least 900 people have perished in the Mediterranean this year according to UNHCR, which on Monday made a fresh appeal to the European Union to re-start its naval mission the Mediterranean.
The EU''s Sophia mission was suspended in March amid protests from the Italian government over the mission's rules of engagement requiring migrants to be landed at the nearest safe port - almost invariably in Italy.
Italy's populist government has closed the country's ports to migrant rescue vessels and imposed fines of up to one million euros on the operators and owners of boats that enter national territory without permission.
