After a year-long trial, Magistrate Wendy Rangan pronounced the verdict saying that there were not enough concrete evidence to prove the suspects were guilty.
The Director of Public Prosecution (DPP) plans to lodge an appeal against the judgement.
The 12 men were suspected of committing an act of piracy in early January 2013 on a merchant vessel MSC Jasmine 260 miles off the Somali Coast.
When the attack happened on 5th January, the master of the merchant vessel sent out a distress call reporting that he and his crew were coming under attack by six men in a fast moving boat, armed with rocket propelled grenades.
However, having employed avoidance tactics, the merchant vessel was able to repel the attack.
The EU Naval Force managed to apprehend suspect pirates at sea, and after engaging with Mauritian authorities, who hold a transfer agreement with the EU, the twelve men were transferred to Mauritius for prosecution.
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