A joint investigation with police had not established any criminal responsibility in the conduct of those running the Sea Watch 3, said a statement from Catania prosecutor Carmelo Zuccaro.
Sea Watch was detained at the Sicilian port for breaching navigation safety and environmental laws, the Italian coastguard reported Friday.
The prosecutor's analysis of their conduct — from when they saved the migrants on January 19 to their arrival at Catania on Thursday — concluded that all their actions had been justified.
The court had nevertheless opened an investigation into illegal immigration which, while not naming anyone in particular, was directly mainly at human traffickers, as happens with all migrant arrivals.
Zuccaro's ruling represents a setback for Italy's far-right, anti-migrant interior minister, Matteo Salvini. He insisted earlier this week that he had all the evidence required to prove the crew had committed offences.
Salvini said on Wednesday that he was looking at ways to ban migrant rescue ships from Italian waters.
Sea Watch 3 was only allowed to anchor in Catania after six other countries agreed to take in the migrants, who include 15 minors.
The crew of the Dutch-flagged ship had expected the vessel to be detained or impounded as a show of strength from Salvini. Zuccaro himself has made a name for himself as a legal thorn in the side of migrant rescue organisations.
In March 2018 he impounded the Open Arms ship while investigating the crew for allegedly aiding illegal migrants by refusing to hand them over to the Libyan coastguard.
The ship was released after a month following a court ruling that Libya could not be considered a safe country because of a lack of safeguards for human rights, but the investigation continues.
Saturday's statement from Catania is in line with a similar one issued at Syracuse, a Sicilian city that cleared Sea Watch of any wrongdoing after holding the boat for several days.
Sea Watch 3 is still being held in Catania however, until the question of the alleged offences reported by the Italian coastguard Friday have been resolved.