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.
Accordingly, the boat had been carrying Egyptian, Sudanese, Eritrean and Somali migrant. Rescue workers have saved 154 people, meaning about 400 could still be missing.
It was not immediately clear where the boat had been heading. Officials said they believed it was going to Italy.
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.
More and more people have been trying to cross to Italy from the African coast over the summer months, particularly from Libya, where people-traffickers operate with relative impunity, but also from Egypt.
Some 206,400 migrants and refugees have crossed the Mediterranean this year, according to the International Organization for Migration.
More than 2,800 deaths were recorded between January and June, compared with 1,838 during the same period last year.
World leaders, including Egyptian President Abdel Fattah al-Sisi, gathered in New York this week at the United Nations General Assembly to discuss the migrant crisis.
