According to the Italian court, a recent decision by the EU Court of Justice means that twelve of the people taken to Albania last week do not meet the criteria for accommodation in Albania.
These migrants, who come from Bangladesh and Egypt, will now be taken back to Italy.
The setback for the migration plan is the second after it was put into operation on Monday. Earlier in the week, four of the original 16 people who arrived in Albania were found to be "vulnerable" and were subsequently taken back to Italy.
The agreement states that migrants caught by Italian ships within the country's search and rescue area are to be taken directly to Albania, where they will be held pending a decision on asylum - with the exception of those considered vulnerable according to the law.
Italy recently expanded its list of "safe" countries of origin to 22, which are defined as states where it is not considered that, for example, torture or persecution occurs that would justify granting asylum. However, the list also includes nations with areas that are not considered safe.
A new ruling from the EU Court of Justice, however, states that EU member states can only designate entire countries as safe, not parts of them.
Meloni's far-right party, Brothers of Italy, is criticizing the Italian court's decision.
