Updated 12.28am

A sailboat belonging to Italian charity Mediterranea has rescued 55 people including pregnant women and children in distress off the Libyan coast, the charity said on Thursday.

"All 55 survivors have been rescued and are now aboard," Mediterranea, which is made up of left-wing activists, tweeted.

"Among them 11 women (three pregnant) and 4 children.... Happy to have rescued 55 lives from the hell of Libya. Now we need a safe port."

The Maltese and Italian governments later agreed that Malta would transfer the 55 migrants to an Armed Forces of Malta vessel which will bring them into Malta.

However, Italy will take 55 migrants currently in Malta.

"This agreement is without prejudice to the situation in which this operation has taken place, and in which Malta has no legal responsibility, but is part of an initiative fostering a European spirit of cooperation and goodwill between Malta and Italy," the government said in a statement.

Italy's far-right Interior Minister Matteo Salvini who has tried to close Italian ports to migrant rescue vessels swiftly tweeted that Mediterranea's small sailboat Alex should take those rescued to Tunisia.

"Otherwise we will activate all procedures to prevent Italy being a port of arrival for human traffickers," Salvini said.

The Italian coast guard later said that the boat had been in the Libyan search and rescue area and that that country had sent a patrol boat to the yacht, the Alex.

Italian authorities last week seized a vessel belonging to German aid group Sea-Watch and arrested its captain after it entered Lampedusa port in Sicily unauthorised with dozens of rescued migrants on board.

Mediterranea said earlier that the Alex was heading for a rubber boat in distress in Libya's search and rescue area. 

Italian authorities informed them that the area was the responsibility of the Libyan coast guard which was sending vessels, Mediterranea said.

"But people must be rescued, not captured and deported back to Libya."

"Libyan patrol boat arrived late, they first asked us to stop, then left the scene," the collective tweeted.

Another makeshift vessel carrying 86 people across the Mediterranean from Libya sank off the Tunisian coast on Wednesday, with all but three of them believed drowned.

Libya, which has been wracked by chaos since the 2011 uprising that killed veteran dictator Moamer Kadhafi, has long been a major transit route for migrants, especially from sub-Saharan Africa, desperate to reach Europe.

On Tuesday night, 44 migrants were killed in an air strike on their detention centre in a Tripoli suburb.

The UN's special envoy on migration in the Mediterranean, Vincent Cochetel, has accused the EU of "blindness" on the plight of refugees and migrants in Libya and called for a rethink of the policy of returning migrants intercepted at sea to the war-torn country