More than 200 people were rescued earlier this week by the Italian coast guard.
According to prosecutors, the suspected duo, both from Africa, could face charges of murder in the wreckage, Xinhua reported.
Prosecutors opined that the two suspects stopped the ship's engines and the operation allegedly damaged the vessel. The ship overturned when people on board started shifting positions in order to avoid falling into the sea.
The shipwreck occurred Monday about 185 km south of Lampedusa island, Italy's southernmost point, and was the latest in a string of similar tragedies in which thousands of Africans have lost their lives.
The survivors claimed that the vessel was ferrying as many as illegal 400 migrants.
According to Frontex, an EU border-management agency, migrants to Italy from Africa were more than 26,000 in the first four months of this year.
Rescue operations for sea patrol missions cost the Italian government more than nine million euros ($12.3 million) every month.