The ship arrived in the southern Italian port of Bari on Saturday afternoon and the migrants were taken to the local hosting centre for asylum seekers .
The court ruling on Friday represents an early stumbling block to a five-year deal between Italy and Albania for Tirana to host 3000 migrants per month picked up in international waters by the Italian coast guard.
They will be vetted for possible asylum in Italy or sent back to their countries.
Italian Prime Minister Giorgia Meloni has hailed the deal as a new "model" to handle illegal migration.
On Thursday, European Union leaders agreed to a tougher stance on migration during talks in Brussels and are pushing to speed up returns of migrants illegally entering the bloc.
Insieme al Primo Ministro di Danimarca — Giorgia Meloni (@GiorgiaMeloni) @Statsmin Mette Frederiksen, e dei Paesi Bassi @MinPres Dick Schoof ho ospitato un incontro per parlare di contrasto dei flussi migratori irregolari e in particolare di soluzioni innovative, in vista del Consiglio Europeo di oggi a… pic.twitter.com/iTou8I9FOJOctober 17, 2024
The court in Rome rejected the detention of 12 of the migrants, arguing that their countries of origin — Bangladesh and Egypt — were not safe enough for them to be sent back.
The Italian navy ship took the 12 from the port of Shengjin, 66 kilometres northwest of Tirana.
After arriving there this week, the four other migrants had already been rejected by centre staff, two as vulnerable after undergoing health checks and two for being minors.
Under Italian law, each migrant's detention must be reviewed by special courts.
Meloni slammed the judges following the ruling, and said that deeming countries such as Bangladesh and Egypt unsafe means that virtually all migrants would be barred from the Albania program, making it unworkable.
Interior Minister Matteo Piantedosi said the government would appeal the ruling.
Speaking to reporters during a trip to Lebanon, Meloni said she would convene a cabinet meeting Monday to discuss the issue.
"We'll meet to approve some norms that will allow us to overcome this obstacle," Meloni said.
"I believe it's up to the government and not magistrates to establish which countries can be considered safe."
Although Bangladesh and Egypt are not at war or facing any large refugee crises, the judges in Rome said their decision was based on recent international rulings that consider discrimination or persecution in even a part of a country as grounds for such a determination.
Italy has agreed to welcome those migrants who are granted asylum, while those whose applications are rejected face deportation directly from Albania.
The controversial agreement to outsource the housing of asylum-seekers to a non-EU member country has been hailed by some countries that, like Italy, are experiencing a high level of migrant arrivals.
The agreement was endorsed by European Commission President Ursula von der Leyen as an example of "out-of-box thinking" in tackling the issue of migration into the European Union.
Human rights organisations considered it as setting a dangerous precedent.
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