The 58 migrants on board the rescue shop Aquarius are expected to be transferred onto an Armed Forces patrol boat and brought into Maltes waters in two days time, when the weather situation improves, Prime Minister Joseph Muscat said.
The governments of France and Malta on Tuesday took a joint initiative to solve the current impasse which has seen the Aquarius stranded in international waters.
A statement on Tuesday said that "the Government of Malta is participating in this effort on purely humanitarian grounds and without prejudice to its position on SAR activities, which remain unchanged."
Malta and France are two of five European Union countries struck a deal Tuesday to distribute between them 58 migrants rescued in the Mediterranean Sea and left stranded by continuing disagreements in the bloc over how to cope with the influx of people trying to enter illegally from North Africa. Spain, Portugal and Germany are the other three nations.
The breakthrough came after days of uncertainty, with EU countries either reluctant to act on the divisive migrant issue or determined to halt the migrant flow. Humanitarian boats loaded with rescued migrants are increasingly shunted between European governments under political pressure to stem newcomers.
All the migrants from the Aquarius 2 rescue ship will disembark in Malta, and Spain will take 15 of the passengers, according to the official. Earlier, Portugal had said it would take 10 of the migrants. The other EU countries did not immediately specify how many they would accept.
Malta said it would send a military boat to take the migrants to shore, before they proceed to the other European countries.
Because the ship had its Panama registration flag yanked earlier, it will sail to its home port in Marseille, France, to "rectify its stateless position" after the migrants disembark, the Maltese government said in a statement.
Humanitarian groups SOS Mediterranee and Doctors Without Borders operate Aquarius 2. It is the sole private rescue boat operating near the deadly central Mediterranean human trafficking route, and Panama's decision to remove its registration threatened to put it out of action.
Panama's maritime authority said it made the move after Italy's anti-migrant leaders complained the boat's captain failed to follow orders. It said Italy argues the captain of Aquarius 2 defied instructions to return migrants to Libya that it had rescued from unseaworthy vessels launched by Libyan-based traffickers.
But the humanitarian groups say violence-wracked Libya doesn't meet international standards for safe harbour.