The boat sank in the Mediterranean Sea off Burg Rashid, a village in the northern Beheira province. Officials said 31 bodies had been found, 20 men, 10 women and one child. A Reuters correspondent later saw a fishing boat bring in 12 more bodies, bringing the total so far to 43.
Rescue workers have so far saved 154 people, officials said, meaning about 400 could still be missing.
The boat had been carrying Egyptian, Sudanese, Eritrean, and Somali migrants, officials said.
At a coastguard checkpoint in Burg Rashid, where the Mediterranean meets the Nile, dozens gathered, anxiously waiting for news of missing relatives.
Egyptian Prime Minister Sherif Ismail said all resources possible would be directed into the rescue mission and that those responsible had to be brought to justice.
It was not immediately clear where the boat had been heading. Officials said they believed it was going to Italy.
