The captain of the migrant rescue ship MV Lifeline will be charged in court, Times of Malta has learnt. 

It was initially believed that the captain would be released on bail after a six-day ordeal at sea but he was informed on Thursday afternoon to attend court on Monday morning, according to a local legal representative. 

The captain will be charged mainly with issues related to the vessel's registration, Aditus director and human rights lawyer Neil Falzon told Times of Malta. 

He was interviewed at the police headquarters on Thursday and the vessel has been impounded pending investigation, a government spokesman told Times of Malta. 

A government spokesman confirmed the captain would be charged but gave no further details. 

The vessel docked at Malta on Wednesday evening, bringing to an end a saga that saw 234 migrants stranded at sea for six days. 

Permission for the ship to dock was granted after eight EU member states agreed to distribute the migrants among them. On Thursday morning, Norway offered to host some of the migrants as well.

The captain of the boat has been criticised for having picked up migrants in Libyan waters, with both Italy and Malta saying he violated international law and initially refused to allow it entry.

The vessel had several children on board. Photo: Jonathan Borg

Asked whether Malta believed Libya provided a "safe port" for asylum seekers, the spokesman said "Malta follows international rules".

But the Lifeline has already given its version as to why it defied orders to hand over the rescued people to the Libyan coastguard since doing so would have not been in line with the Geneva Refugee Convention and therefore criminal.

The ship received the reply to disembark in Tripoli, which would have been a breach of the principle of non-refoulement, which is the practice of not forcing asylum seekers to return to a country in which they are liable to be subjected to persecution.

Lifeline said it would obey all instructions received from different maritime authorities as long as it was in compliance with international law.

Government toughens up on port entries

Meanwhile, the government said that following the recent events that brought to the fore information that was "previously unknown", Malta needs to ascertain that operations being conducted by entities using its port services and operating within the area of Maltese responsibility are in accordance with national and international rules.

"This includes, but is not solely limited to, the certification or registration of vessels involved."

It said that given there are investigations being carried out by independent authorities, and until these issues are clarified, Malta cannot allow entities, whose structure might be similar to that being subject to investigations, to make use of Malta as their port of operations, and to enter or leave the port.

"This is also in view of judicial processes that might ensue, and in order for the Maltese authorities not to be considered to be approving of systems of operations that might eventually be found to be carried out in breach of their own and international rules."