Insufficient evidence to prove that they were pirates was the reason behind the ruling.
The three men were arrested alongside 23 more suspected pirates off the Horn of Africa, in January 2012.
Two of the three acquitted men were appealing against their 21-year sentence and the third, a 16-year-old, had received a sentence of 14 years.
According to reports at the time, the Danish navy freed 14 Iranian and Pakistan hostages who were being held hostage on the ship on which the 25 Somali men were captured.
Local media cite the suspected pirates’ lawyer saying that the fact that they were caught in international waters made it hard to gather evidence to prosecute them. They will now be repatriated.
Over the last two weeks, two court decisions – one in France and one in Denmark – have given alleged pirates compensation over violation of their human rights.
Statistics from the Seychelles show that some 111 Somali pirates from the local prison have been repatriated to either the Garowe (Puntland) and Hargeysa (Somaliland) prisons, two detention facilities built by the United Nations Office on Drugs and Crimes.
But a total of 41 Somali pirates were still being held in the Seychelles as of October.