Malta's ports will no longer allow entry to ships carrying migrants that are operated by NGOs, a government spokesman has confirmed to Times of Malta.

In a cryptic and legalistically-worded statement on Thursday, the government said "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 to national and international rules".

Asked whether the statement signalled that Malta’s ports were now closed to NGO ships that rescue hundreds of migrants, the spokesman confirmed on Friday this was the case "unless there are NGO boats registered according to laws".

The statement is clearly intended to place NGOs vessels in a legal quagmire that could last weeks.

The government spokesman told Times of Malta that this measure would remain in place “pending reviews and current investigation”. 

The Aquarius, the NGO operating a migrant rescue vessel ship already said it had been denied entry into Malta for re-supply and a change of crew.

On Wednesday, Malta let the charity ship Lifeline dock with 233 migrants on board. The vessel was was stuck at sea for almost a week after Italy closed its ports to NGO rescue vessels.

Prime Minister Joseph Muscat announced Malta would let the ship dock after eight other countries agreed to take some of the migrants, noting this was a one-time “ad hoc” solution.

Meanwhile, the captain of the Lifeline is expected to be charged in court in the coming days after it was initially believed that the captain would be released on bail after the six-day ordeal at sea. He was, however, informed on Thursday afternoon to attend court on Monday morning.

Read: Migrant rescue boat captain to be charged on registration issues

The captain will be charged mainly with issues related to the vessel's registration.

The closing of Malta’s ports to NGO vessels comes as EU leaders meet in Brussels for a summit that has so far been dominated by migration issues that have left member states in disarray in recent weeks, resulting in standoffs between Malta and Italy and problems among other traditional allies.

European Council president Donald Tusk announced earlier this morning that European leaders had reached a deal on migration in the early hours of Friday after tense and lengthy talks, but the pledges made to strengthen borders were vague, with German Chancellor Angela Merkel conceding differences remained.