"The vessel Vega rescued 135 migrants from a sinking vessel. Forty-five bodies were recovered and search efforts are ongoing," the navy said on Twitter.
The latest tragedy struck just a day after up to 30 people were believed to have died in another shipwreck.
And in one of the worst such incidents in the Mediterranean recently, a fishing trawler with some 650 people capsized off the coast of Libya on Wednesday.
The Italian navy, which captured the tragedy in a horrifying video that shows the boat roll over and dump its passengers into the water, was able to rescue about 560 people.
"Three sinkings in three days, it's very worrying," said Carlotta Sami, spokeswoman for the UN refugee agency in Rome.