Two teenage migrants charged with "terrorist activity" after being charged with taking over a commercial vessel are being held at the main prison in Paola, in breach of the magistrate's orders, Times of Malta has learned.

The minors were meant to be held at the prison youth section in Mtaħleb, rather than at the adults' prison in Paola, after being arraigned on Saturday and accused of seizing control of the vessel through the use or threat of force and intimidation.

If found guilty, the two teenagers - aged 15 and 16 - face between seven and 30 years behind bars. 

Contacted about the incident, lawyer Neil Falzon said apart from the fact it was shameful that the two were facing terrorism charges it was also shameful that, pending the procedures, their special protection needs were being totally ignored. 

On Saturday, magistrate Donatella Frendo Dimech ordered the two minor suspects to be entrusted to State care and everything done to ensure their safety and well-being. 

"Tomorrow morning we will be taking the necessary action to ensure that our clients are protected according to law," he said on Thursday. 

Another, aged 19, was also arraigned on the same charges. The three teenagers have pleaded not guilty to the charges and requested bail.

The case made international headlines after the captain and crew of a Turkish merchant ship had rescued some 100 people stranded at sea. The three allegedly forced the captain to change the vessel's route to Malta, instead of Tripoli. 

Malta's Armed Forces stormed the ship when it was close to the country's waters after the captain insisted he was not in control of the ship.

A pregnant woman, a child of six months and 47 people claiming to be minors were among the rescued aboard the ship.