Six other Pakistani passengers were rescued after the boat hit a bridge late on Tuesday as Muslims prepared to celebrate the Eid al-Fitr festival that marks the end of Ramadan, General Hamed al-Oqaili told AFP.
Emergency teams recovered the body of the drowned man. They were continuing to search the waters for the three missing passengers — a woman and her two children.
Accidents are common on the Nile, which is used by many cargo vessels and ferries as well as pleasure boats.
Earlier this year, 15 people drowned when an unlicensed ferry sank.
Last year, 40 people died when a pleasure boat collided with a cargo vessel.