A Spanish warship which was refused entry in Malta to disembark some 100 migrants has transferred the migrants to a Tunisian warship. 

The destroyer Admiral Juan de Borbon was just outside Maltese territorial waters in the past two days as Malta, Spain and Nato argued over the situation.

It left for Tunisia late yesterday and transferred the migrants to a Tunisian warship this morning, just outside Tunisian waters.

"The Government of Malta thanks all parties directly involved in the logical conclusion to this search and rescue operation," the Ministry of Home Affairs said in a statement.

The migrants were picked up off Libya on Sunday, 78 nautical miles from Tunisia, 88 nautical miles from Lampedusa and 141 nautical miles from Malta.

The government insisted that the migrants should have been taken to the harbour  that was closest to the rescue position. On Thursday it asked Nato for an explanation as to why the warship headed for Malta, but none was given.

Home Affairs Minister Carmelo Mifsud Bonnici said on Thursday Malta was only informed that the migrants were being brought here 18 hours after the rescue and when the Spanish ship was just 40 nautical miles from the island.

Malta asked the Nato command in Naples to explain why the immigrants were being brought here and whether similar requests for disembarkation were made to Tunisia and Italy. The Spanish government said  the destroyer never received instructions from Nato to go to any particular country. 

The migrants had to be rescued after the engine of their boat failed. A tug boat tried assist them but its crew was unable to repair the engine.