It says the coast guard received a call for help today from a boat carrying the migrants and naval forces went out to the rescue.
The agency said the survivors were 72 Palestinians, 40 Syrians, and four Egyptians. The nationalities of those who drowned were not immediately available.
Officials said rescue efforts continued.
At least 70,000 Syrians are registered in Egypt as refugees. Many non-registered, including thousands of Palestinians who also fled the war in Syria, use the country as a stop before making the perilous sea trip to Europe.