Malta had refused to take in 26 migrants on Monday after they were picked up by a Spanish tug-boat in rough seas.
Earlier Michael Frendo, the Maltese foreign minister, told a meeting of the foreign ministers of the Mediterranean Forum attended by Libya that they had a duty towards the migrants.
"All countries around this table have a duty to save lives at sea in the search and rescue zone for which they are responsible," Frendo said in Crete.
Hundreds of would-be migrants are feared to have drowned after trying to cross in rickety boats to find work in Europe.
On Friday a French navy ship found around 20 bodies floating off Malta.
Last week 27 shipwrecked Africans spent three days clinging to tuna nets in the Mediterranean while Malta and Libya argued over who should rescue them.