Witnesses said they saw troops loading dozens of bodies onto trucks.
Government forces appear to have regained control of the city after Friday’s demonstrations, but the situation is still said to be tense.
There are rebel gunmen based in the city’s administrative headquarters, according to some reports.
Angry residents denounced the authorities.
Friday saw troops open fire on huge crowds and exchange fire with armed protesters.
Uzbek officials refused to negotiate with the protesters, who they branded as “rebels”.