By next year, some 4,000 artifacts will be exhibited at the museum.
They will be displayed in chronological order with visual animations that will take visitors back in time.
Lifesize wax sculptures will show visitors how cavemen lived on the banks of the Tigris River.
The museum will also house a cafeteria, foyer, conference hall, library and children's area.
"We have transferred many works, especially from the old settlement area of Hasankeyf, to a newer archaeology park. Miniature models of these works will be displayed at the museum," said Ali Rıza Altunel, deputy director general of cultural heritage.
Hasankeyf, 32 kilometers (20 miles) southeast of the provincial capital, Batman, was declared a conservation area in 1981.
There are nearly 6,000 caves around the town which provide an insight into the Christian and Muslim civilizations that inhabited the region.
It also has a Byzantine fortress.
The museum includes artifacts excavated by teams from the Ilısu Dam, a project that will generate electricity for southeastern Turkey.
As teams started filling the dam downstream, the historic city of Hasankeyf had to be evacuated.
