SOS Mediterranee in a statement said that because of the recent refusal of Italy and Malta to let rescue vessels carrying migrants dock, ships might be now unwilling to get involved fearing they will be stranded with migrants aboard and denied a port to disembark them. She said "it could of course be the case that in theory a flag state of a rescue ship could be considered a potential location for disembarkation, but this might not be possible in practice". More than 650,000 migrants have come to Italy's shores since 2014.
Over the past few months, southern European countries have taken a hard line on those rescued as they try to cross the Mediterranean, refusing to allow ships to dock and the migrants to disembark.
The Aquarius faced a similar issue in June, when it rescued 630 migrants and delivered them to Spain - again after Malta and Italy declined to accept them.
In June, Aquarius was forced to sail north for days with more than 600 migrants to Spain after Italy and Malta refused it docking permission.
Italy's transport minister has called on the United Kingdom to take responsibility for 141 people rescued by a ship sailing under the flag of the British territory of Gibraltar.
The European Commission was in touch with several EU states and is trying to help resolve the "incident" with the Aquarius, a spokesperson in Brussels said.
Migrants are seen resting on board the MV Aquarius rescue ship run by SOS Mediterranee organisation and Doctors Without Borders during a search and rescue (SAR) operation in the Mediterranean Sea, off the Libyan Coast, August 12, 2018.
"Malta was neither the coordinating nor the competent authority (and).the requests for the vessel to enter our ports are unwarranted and without legal standing", it said in a statement. Those rescued in recent years have said they receive scanty rations while kept in Libya to await the opportunity to leave on human smugglers' unseaworthy boats. "Spain is not the safest port", sources close to Spain's prime minster were reported saying by El Pais.
Though departures from Libya have fallen dramatically this year, people smugglers are still pushing some boats out to sea and an estimated 720 people died in June and July when charity ships were mainly absent, Amnesty International estimates.
The government also pointed out that a further 114 migrants were rescued at sea and brought to Malta on Monday.
For years, Italy pleaded with its European Union partners for help with a massive influx of arrivals from Africa that has seen 700,000 people cross the Mediterranean and land in the country since 2013.