More than 800 passengers were still missing 36 hours after the Al-Salam Boccaccio 98 sank while sailing from the Saudi port of Duba to Safaga.
The violence erupted after riot police moved in to control the angry crowd and were pelted with stones.
Some police responded by throwing projectiles back towards the demonstrators.
Police rushed the crowd several times, and formed a cordon to keep relatives away from the port gates.
A stream of ambulances ferried the injured to hospital.
After visiting survivors in hospital, President Hosni Mubarak met with Prime Minister Ahmed Nazif to discuss the tragedy.
Some survivors say a fire broke out below deck shortly after the 35-year-old ship left Duba on Thursday evening.