A court ruled the company will have to pay a fine of €1 million ($1.3 million) and will no longer be investigated for alleged responsibility in the disaster. Costa will instead aim to take part in the expected trial as an injured party.
"It is a balanced solution," the company's lawyer, Marco De Luca, told reporters in Grosseto in Tuscany where the court hearing was held and where preliminary hearings will begin on Monday to decide whether the accused should face trial.
Prosecutors have levied charges against six people including captain Francesco Schettino and the head of Costa Crociere's crisis unit Roberto Ferrarini for the January 2012 incident. The charges have to be confirmed before any trial can go ahead.
The giant luxury liner crashed into the Italian island of Giglio with 4,229 people on board just as many passengers were dining on the first night of their Mediterranean cruise, prompting a panicked and chaotic night-time evacuation.
Dozens of passengers are suing the company for damages, although most of those who were not injured or did not lose loved ones have accepted €11,000 in compensation from Costa, which belongs to US giant Carnival.
Wednesday's ruling bears only on the criminal investigation and not on civil proceedings.