The teenagers, among 108 refugees and asylum seekers rescued by El Hiblu 1 earlier this week, appeared at a court in the Maltese capital, Valletta, on Saturday.
They were accused of seizing control of the tanker and using force and intimidation against the crew to change the ship’s course to Europe.
Under Maltese law, unlawfully taking control of a ship is punishable with prison terms of between seven and 30 years.
The suspects pleaded not guilty and were placed in preventive detention pending trial.
The Valletta court identified one of the accused as Abdalla Bari, a 19-year-old from Guinea. The other two are a 15-year-old, also from Guinea, and a 16-year-old from Ivory Coast, who as minors could not be named.
The minors told the court they are secondary school students, while Bari said he had been studying sociology before leaving his country.
Nader el-Hiblu, the ship’s captain, said the drama began on Tuesday afternoon when his tanker was travelling from Turkey to Libya. A military aircraft flying above alerted him of a boat with people who needed help, he told The Associated Press news agency.
He was not sure if the aircraft was Maltese or Italian.
Once the refugees and migrants were on board, the ship continued its course towards Libya, a country where the United Nations and aid groups say refugees and asylum seekers face trafficking, kidnap, torture and rape.
But on Wednesday, when those rescued realised they were headed back to the country they had just left, some revolted, commandeering the ship and forcing it to head to Europe.
The hijackers “were desperate and absolutely did not want to return” to Libya, el-Hiblu said. They “attacked the cockpit, heavily beating on the doors and the windows and they threatened to smash the boat”.
He called the port in Libya, informed them of the hijacking, and told them the crew was heading north towards Europe.
A Maltese special operations unit boarded the ship a day later, arrested five men suspected of leading the hijacking. They handed control back to the captain who steered the ship to Valletta under a navy escort.
Matteo Salvini, Italy’s anti-immigration interior minister, described the incident as an “act of piracy”, but some aid groups called it an act of self-defence against Europe’s immigration policies, which aim to ship back desperate refugees and migrants back to Libya.
In recent months, boatloads of rescued people have refused to disembark there, prompting local authorities to use force.
The European Union member states have been at loggerheads over migration since a spike in the Mediterranean arrivals caught the bloc by surprise in 2015, stretching social and security services and leading to support for far-right, nationalist and populist groups.
In 2018, 2,262 people died at sea while trying to reach Europe, the UN said.
The perilous journey has killed 311 people so far this year, according to the Missing Migrants Project, an NGO that tracks the deaths of migrants, refugees and asylum seekers along international migration routes.
Sea arrivals have fallen from more than a million in the peak year of 2015 to some 140,000 people last year.
But political tensions around migration run high in the EU, and have flared once more ahead of the European Parliament election in May.