Lorries took the bodies from the jail in Comayagua to the mortuary in Tegucigalpa, 100km (60 miles) away.
Relatives have travelled to the capital to wait to recover the remains of their loved ones.
The government has promised a full investigation and accepted that the entire prison system needs reform.
A spokesman for the public prosecutor’s office said the final toll was now at 355 – the world’s worst prison fire in a century.
“That is the total brought from the facility, and there were no more,” said Melvin Duarte.
Overnight 115 corpses were brought to the capital and a further 238 in the morning. Two prisoners died in hospital.
Foreign experts are joining Honduran colleagues to help identify the bodies, many of which were so badly burned that dental records and DNA will be needed.
Honduras prison fire: Families’ grief and anger
Survivors said inmates had tried to save themselves by jumping into showers or sinks as the fire spread on Tuesday night.
“I woke up with all the screaming from my fellow inmates, who were already breaking the wood and zinc ceiling,” one survivor said.
Families gathered at the scene when news of the fire broke.
Anger grew and at one point some relatives clashed with police as they tried to force their way into the building.
Firefighters said they could not get the prisoners out because they could not find the guards who had the keys to the cells.
Minister for Public Works, Miguel Rodrigo Pastor, said the fire was started by two inmates having a fight. President Porfirio Lobo has pledged a “full and transparent” investigation.
He has also suspended local and national prison officials while the inquiry is under way.
Some survivors told investigators that an inmate started the blaze by setting fire to his mattress. Authorities are also looking at whether there was an electrical fault.
Whatever the cause, the Honduran government has said the prison system needs to be overhauled.
But similar promises were made in 2004 when a fire at a prison in San Pedro Sula left 107 inmates dead.
Prisons in Honduras, which has the world’s highest murder rate, hold some 13,000 inmates in a system designed for 8,000.
The country enacted strict anti-gang legislation several years ago to tackle the violent street gangs known as maras.
But critics say this can lead to people being jailed for just sporting a gang tattoo.
More than half the inmates in Comayagua were on remand or held as suspected gang members, the Associated Press says.
AP obtained an internal Honduran government report sent to the United Nations that detailed conditions in the Comayagua prison.
The report said that there were some 800 prisoners in a jail built for 500, and only 51 guards by day and just 12 by night.
The Central American nation, which lies on key drug-trafficking routes, has also seen a rise in organised crime.
“Due to the drug traffic that happens in our country the number of inmates has increased rapidly and our response, our economic capacity to respond to that increase hasn’t been enough,” Honduran Foreign Minister Arturo Corrales told the BBC.