Mare Jonio was inspected in Marsala port in Sicily by members of the coastguard specialised in navigation safety.
The boat was sanctioned for irregularities on board, the coastguard said in a statement, concluding that the ship did not meet rescue operation standards.
It comes after Italy's far-right Interior Minister Matteo Salvini last week signed a directive against charity vessels rescuing migrants off Libya, targeting the Mare Jonio in particular.
Salvini, head of the anti-immigrant League party, had warned that the Mare Jonio and others must obey the orders of authorities in foreign search and rescue regions — a reference to the Libyan coastguard.
The Mare Jonio rescued 49 migrants off the North African country in March after refusing to wait for a Libyan coastguard boat that was in the vicinity.
It took them to the Italian island of Lampedusa, where the ship was temporarily seized by the authorities as part of a probe into illegal immigration, before being given the all clear.
There has been concern in Italy that recent violence in Libya will spark an exodus of people determined to seek safety in Europe.
Salvini has repeatedly said Italian ports are closed to all those attempting the perilous Mediterranean crossing.