The court said that the 12 men from Bangladesh and Egypt must be brought to Italy to have their asylum applications processed because their countries of origin are not safe, making them ineligible for the new migration scheme.
The men were part of the first group of 16 migrants who were taken on board an Italian navy ship to Italy's offshore asylum processing centre on Wednesday.
Four men from the group were then transported to Italy because they were either minors or had significant health problems.
It was initially unclear whether the remaining 12 men would be brought to Italy immediately or whether the case would be referred to a higher court.
Italy is the first country in the European Union to set up centres for refugees outside the EU.
Under the new system, migrants headed for Italy across the Mediterranean are brought to the Albanian port of Shengjin for an initial screening before being transferred inland to the main camp in nearby Gjader.
Those deemed entitled to asylum are allowed to continue to Italy while those denied it are repatriated to their country of origin.
However, only adult men from countries of origin that are classified as safe and who are picked up in the Mediterranean by Italian authorities will be taken to the processing centres under the scheme, which also sets out that women and children as well as those who are sick or show signs of torture will not be transported to the centres, nor will those who reach Italy's shores on their own or on private ships.
The scheme is an attempt by the government of Italian Prime Minister Giorgia Meloni to tackle irregular migration.
Meloni called a cabinet meeting for Monday to decide on the government's response to the legal ruling.
Italy is one of the countries most affected by migration from Africa to Europe across the Mediterranean, with 160,000 migrants reaching Italy's shores by boat last year, according to the Italian interior ministry.
Although the number of people arriving in Italy is currently less than half what it was one year ago, tens of thousands are still setting out across the Mediterranean in boats that are often barely seaworthy.
Other EU countries are closely monitoring the Italian scheme, as many attempt to tighten their migration policies.
with Reuters
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