"We are pulling out bodies," said prisons director Danilo Orellana about the fire in the country's overcrowded prison system that also left score of inmates injured.
"The situation is serious. Most have suffocated," Orellana said of the fatalities, adding that the fire did not appear to have been caused by a riot.
Honduran officials said the number of dead could surpass 300, and that of the more than 850 inmates housed in the prison, 357 were unaccounted for, although they noted some might have escaped during the fire.
Meanwhile, hundreds of the inmates' distraught relatives -- frustrated over being left in the dark about the fate of their loved ones -- clashed with police and then stormed the prison.
Some 300 men, women and children rushed through the gates of the prison in Comayagua when police withdrew after failing to contain the crowd of family members, who gathered at the facility hours after a huge fire roared through the cells, asphyxiating many prisoners.
The blaze broke out at around 10:50 pm Tuesday (0450 GMT Wednesday), and took about three hours to bring under control.
Orellana said investigators were looking into whether it was caused by an inmate or by a short circuit.
"We're bringing in all of our forensic equipment," he said.
Witnesses said some of the inmates escaped the blaze by jumping from the prison rooftop, and there were reports that some of them had fled the facility and were on the loose.
The prison, located some 90 kilometers (56 miles) north of the capital city of Tegucigalpa, held almost double its official inmate capacity.
The facility also is located some 500 meters (1,650 feet) from a highway that links San Pedro Sula, the economic center of Honduras, with the capital city Tegucigalpa.
Authorities said police helped to evacuate other inmates from the facility, which also functions as an agricultural complex dedicated to animal husbandry and raising crops.
Prisons in Honduras -- as is the case throughout Latin America -- are notoriously overcrowded. The country's 24 overcrowded penal facilities officially have room for 8,000 inmates, but actually house 13,000.
The crowding and appalling living conditions are a cause of the frequent riots which break out across the region, and also a source of frustration for angry and exasperated relatives.
At the break of dawn Wednesday, hundreds were lined up at the prison gates seeking information about the tragedy before the crowd grew restive and began throwing stones at police.
Security forces shot into the air in a bid to stop the unrest, but the relatives burst through a locked gate and flooded into the facility, where they gathered in a front courtyard.
Before crashing the gates, the family members expressed outrage over delays by firefighters and other emergency personnel, and the lack of information from officials.
"My brother Roberto Mejia was in unit six," said an emotional Glenda Mejia.
"They've told me that the inmates from that unit are all dead," she told AFP.
Nearby, Carlos Ramirez was waiting outside the facility for word about his brother Elwin, imprisoned on a murder conviction, who also was housed in unit six.
"I haven't been told anything," Carlos Ramirez said, his voice breaking.
Officials here expressed sympathy with the relatives' frustration, but urged them to be patient.
"We understand the pain of the families, but we have to follow a process under the law," Security Minister Pompeyo Bonilla told local media.
"We call for calm. It is a very difficult situation," he said.