In a statement, the Maltese government said the migrants had been intercepted while trying to cross the Mediterranean Sea on a rubber dinghy some 68 nautical miles south of Malta.
It said the AFM had rescued the migrants, whose dinghy was taking on water and was going to sink.
In addition to the 100 migrants that were found alive, the Maltese government said the AFM had also brought two corpses back to Malta.
Migration has been thrust to the top of the European agenda in recent months, after Italy's new populist government changed its policy on receiving migrants. Italy refuses any boats carrying migrants and asylum seekers.
On Tuesday, Italian interior minister Matteo Salvini accused Malta and a host of other European countries of failing to take in their share of a group of over 400 migrants that were allowed to disembark in Pozzallo last month. Salvini said that so far only France had taken in its share of the migrants.
However, the Maltese government said this was not the case and that Malta had been in touch with Italian authorities in order to fulfill its obligations as soon as possible.
"Nevertheless, the Italian authorities have not provided any tangible procedure for Malta to follow," read the Maltese statement.
It added that on the other hand, it was "unfortunate" to note that "Italy has not yet fulfilled its commitments on the redistribution mechanism initiated by Malta with respect to the migrants" which landed in Malta on the MV Lifeline back in June.
"Malta always participates in solidarity mechanisms and was the first European Union member state to fulfill its commitments with regard to the European Commission's solidarity mechanism with respect to Italy and Greece," the Maltese government said.
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