The Sea Story left port near the eastern town of Marsa Alam on Sunday for a five-day diving trip, officials said.
The boat with 44 people on board sent a distress signal at 05:30 (03:30 GMT) on Monday, according to the governor of the Red Sea governorate.
Maj-Gen Amr Hanafi said the boat sank within five to seven minutes.
Survivors were found in the Wadi el-Gemal area, south of Marsa Alam, he added.
On Saturday, the Egyptian Meteorological Authority issued warnings about turbulence and high waves on the Mediterranean and Red seas.
Wind speeds were between 37-43 mph (60-70 kmph), and wave heights were three to four metres (10-13ft) high, they said.