"The prisons have to be governed by law," Maduro said on television early Saturday.
Humberto Prado, an activist who leads the watchdog group Venezuelan Prisons Observatory, said inmates' relatives and media accounts put the toll at 55 killed and 88 injured.
The Venezuelan newspaper Ultimas Noticias and the television channel Globovision reported more than 50 killed, both citing Ruy Medina, the director of Central Hospital in the city.
Relatives wept outside the prison during the violence, and cried at the morgue Saturday as they waited to identify bodies.
Varela said Friday that the riot broke out when groups of inmates attacked National Guard troops who were attempting to carry out an inspection.
Varela said the violence had affected a number of prisoners and officials, but said the authorities would hold off until control had been re-established at the prison to confirm the toll. She said the government decided to send troops to search the prison after receiving reports of clashes between groups of inmates during the past two days.
The death toll provided by Medina rose late Friday after he had initially reported four killed and dozens injured. Ultimas Noticias reported that the victims included a Protestant pastor and a member of the National Guard, as well as inmates.
Opposition leader Henrique Capriles condemned the government's handling of the country's overcrowded and violent prisons.
"Our country's prisons are an example of the incapacity of this government and its leaders. They never solved the problem," Capriles said on his Twitter account. "How many more deaths do there have to be in the prisons for the government to acknowledge its failure and make changes?"
The Venezuelan Prisons Observatory said in a statement that in 2007 the Costa Rica-based Inter-American Court of Human Rights had ordered the government to seize weapons that inmates had in their possession at Uribana prison and to take measures to avoid deaths in the facility. The group called for the government to release a list with the names of the dead and wounded in Friday's violence, as well as details about weapons seized in the search.
"No one doubts that inspections are necessary procedures to guarantee prison conditions in line with international standards, but they can't be carried out with the warlike attitude as (authorities) have done it," Prado told The Associated Press in a telephone interview. "It's clear that the inspection wasn't coordinated or put into practice as it should have been. It was evidently a disproportionate use of force."
Prado's group says Uribana prison was built to hold up to 850 inmates but currently has about 1,400.
It was the latest in a series of bloody riots in the country's severely overcrowded prisons where inmates often freely obtain weapons and drugs with the help of corrupt guards. Venezuela currently has 33 prisons built to hold about 12,000 inmates, but officials have said the prisons' population is about 47,000.
In April and May, a prison uprising in La Planta prison in Caracas blocked authorities from going inside for nearly three weeks. One prisoner was killed and five people were wounded, including two National Guard soldiers and three inmates.
Two months later, another riot broke out at a prison in Merida, and the Venezuelan Prisons Observatory reported 30 killed.
In August, 25 people were killed and 43 wounded when two groups of inmates fought a gunbattle inside Yare I prison south of Caracas.
Chavez's government has previous pledged improvements to the prison system, but opponents and activists say the government hasn't made progress.
Varela, the prisons minister, said news media including Globovision and a local newspaper had run reports on the inspections, which she said had in fact been a "trigger for the violence."
Prado denied that, saying: "The problem isn't the work of the media. The problem is that the government hasn't disarmed the prison population."
Associated Press writer Ian James contributed to this report.