Authorities in the Sicilian port of Trapani detained the Ocean Viking migrant rescue ship following an 11-hour inspection, the group that operates the vessel said Tuesday.
Search and rescue group SOS Mediterranee criticised what it called the "extreme scrutiny", insisting everything was in order.
Italy's coastguard said, however, the inspection had thrown up "various irregularities of a technical nature that could compromise the safety of crew and persons brought aboard".
Citing a "defective system of on-board security management", the coastguard highlighted electrical current irregularities as well as the presence of "inflammable materials" stored in ship quarters not adapted for the purpose.
The authority added that, until those faults were rectified, the vessel would not be released.
The detention comes exactly one year after Ocean Viking returned to the seas following five months spent blocked in Italy over alleged safety issues.
A routine inspection on Monday by Trapani port state control officers found separate issues with the registration of container structures on the rear deck of the Ocean Viking, the group said in a statement.
The structures were added two-and-a-half years ago to shelter survivors and hold the equipment, the group added, insisting they had been "validated by all relevant regulatory bodies".
"We regret the extreme scrutiny our vessel continues to be subjected to," said Frederic Penard, director of operations of SOS Mediterranee.
"This inspection was the sixth port state control the Ocean Viking underwent since starting operations in the central Mediterranean in August 2019.
"This leads to new delays in the resumption of our operations."
Tens of thousands of people seeking to reach Europe cross the central Mediterranean each year, setting off from North Africa in what are often leaky and overcrowded boats.
More than 67,000 migrants arrived on Italy's shores in 2021, according to Italian interior ministry figures.
Overall, the UN refugee agency estimated that around 115,000 arrived by sea last year to Italy, Greece, Spain, Cyprus, and Malta. More than 1,800 were reported dead or missing.