A tanker which was hijacked by rescued migrants was sezied by the Armed Forces of Malta as it tried to enter Maltese territorial waters, the AFM said.

The vessel was later escorted to Boiler Wharf, Senglea, where the 100 migrants disembarked among heavy police and military presence at around 8.30am.

Five of the migrants, believed to be the ring leaders, were immediately arrested by the police and taken to the police headquarters for questioning.

Armed Forces of Malta soldiers, armed to their teeth, were seen on the vessel as it approached shore and monitored the disembarkation process.

Several police and army vehicles were in the area where the migrants disembarked about one hour after the arrival of the vessel. The migrants, except for the arrested persons, were taken to the initial reception centre.

The merchant ship was taking the rescued migrants back to Libya on Wednesday but six miles away from the coast the migrants had taken over control, and changed course north towards Malta or Lampedusa.

Italy's interior minister Matteo Salvini slammed the migrants as pirates but aid groups rejected that label, saying the European Union's policy of sending migrants back to lawless Libya was to blame.

Armed military personnel stood guard on the ship's deck, and a dozen or so migrants were also visible, as the Turkish oil tanker El Hiblu 1 docked Thursday at Boiler Wharf in the city of Senglea. Five suspected ringleaders were led off in handcuffs.

In all, the Turkish tanker rescued 38 males, 15 females, and 47 claiming to be minors, the government said. 

A pregnant woman and a child were taken to Mater Dei Hospital for further medical observation after the disembarcation in Malta. 

The rest of the immigrants were escorted to the Marsa Initial Reception Centre, where their needs will be adhered to.

The five immigrants were arrested and held for police questioning, following the captain’s report.  

The captain and crew are also being questioned. A magisterial inquiry is underway.

The operation was led by the Armed Forces of Malta, the Malta Police Force, the Agency for Welfare and Asylum Seekers, the Civil Protection Department, and the Health Services, the government said.

Photos/video Alenka Falzon

Authorities in Italy and Malta on Wednesday said the group had hijacked the vessel after it rescued them in the Mediterranean Sea off Libya, and forced the crew to put the Libya-bound vessel on a course north toward Europe.

Maltese armed forces established communications with the captain while the ship was still 30 nautical miles offshore. The captain said he was not in control of the vessel "and that he and his crew were being forced and threatened by a number of migrants to proceed to Malta," the armed forces said.

The migrants did not have weapons, but the captain and crew were outnumbered and forced to surrender.

Italian Interior Minister Matteo Salvini on Wednesday described the takeover as "the first act of piracy on the high seas with migrants" as the alleged hijackers.

Salvini, who insisted the ship would not be allowed to dock in Italy, on Thursday praised the Malta's interception.

"Immigration is managed by criminals and should be blocked by any legal means necessary," Salvini was quoted as saying by the Italian news agency ANSA.

The vessel had been hijacked by some of the migrants who did not want to return to Libya, but wanted to go to Europe.

Humanitarian organizations rejected Salvini's characterization of piracy, saying that migrants have been repeatedly mistreated, raped and tortured in Libya. They have long protested EU protocols to return migrants rescued offshore to the lawless northern African nation.

The ship had been heading toward Italy's southernmost island of Lampedusa and the island nation of Malta when Maltese forces intercepted it. The special team that restored control to the captain was backed by a patrol vessel, two fast interceptor craft and a helicopter.

In its operation to seize the vessel, an AFM Special Operations Unit team was dispatched to board and secure the vessel in order to hand over control of the ship to the captain.

The team was backed up by AFM Patrol Vessel P51, two Fast Interceptor Craft, and one the AFM’s AW 139 helicopters.

P21 kept on escorting and monitoring the tanker throughout the operation.

Maltese Prime Minister Joseph Muscat said on Twitter that the AFM had conducted a "sensitive operation on high seas."

"We do not shirk responsibility despite our size," he said, pledging to follow international rules.