One of the person who drowned was a Somali woman and the other was a man from Eritrea. They were trying to cross to Italy through the Borlos Lake via the Mediterranean Sea.
Five others suffered minor injuries and are getting treated at a hospital, a medical officer said.
A security source said that about 300 people from different nationalities, including six Egyptians, were trying to cross over to Italy in a boat.
The Egyptian Coast Guard has arrested about 200 of them. The rescue team, who have pulled out the two bodies, is still searching for the missing people.