"Our hope is that there are no other deaths inside the ruins," Interior Minister Besir Atalay told reporters at the scene.
Atalay initially said four people were killed in the explosion, but later raised the death toll to six.
The explosion ripped off the building's glass-covered facade and shattered the windows of nearby buildings. Twisted metal and concrete slabs were strewn around the nearby area.
NTV news channel showed medics helping an injured man into an ambulance, while passers-by helped another lying on the pavement outside the four-story building.
A witness told NTV he saw dozens of people covered in blood lying on the ground before ambulances arrived at the scene.
Fethi Yasar, mayor for the area, said around half of the factory's 80 workers had escaped unharmed.
Ankara's Mayor Melih Gokcek told CNN-Turk television that the blast was most likely started by oxygen tanks at the factory. He did not give details.
Atalay said the cause of the explosion is under investigation. The blast could be heard several kilometers away.
