The disturbance at the notoriously violent prison in Uribana is the latest incident involving the country's overcrowded prisons, CNN reported Saturday.
Prison advocacy groups said the country's prisons hold about 50,000 inmates, about three times what the facilities were designed for, Voice of America reported.
Prison minister Iris Varela said local media had reported about plans to remove weapons from the inmates. National troops sent to conduct the operation were met with violence Friday.
Prison officials said the reports by news network Globovision and other media were "a detonator for the violence."
Globovision said at least 50 were killed and 90 injured, but the ministry did not release the number of casualties. "Once we have absolute control of the facilities," more details will be released, the prison ministry said in a statement.
The troops were sent to the prison after prison gangs fought this week.
In the first six months of 2012, more than 300 inmates died in Venezuelan prisons, a prison watchdog group said.