The fighting lasted for almost eight hours in the lock-up in the coastal city of Guayaquil and authorities attributed the fighting to prison gangs linked to international drug cartels.

Videos circulating on social media showed bodies, some burned, lying on the ground inside the prison.

Inmates "tried to dynamite a wall to get into pavilion 2 to carry out a massacre. They also burned mattresses to try to to drown (their rivals) in smoke," Governor Pablo Arosemena of Guayas province said.

"We are fighting against drug trafficking," Arosemena said.

"It is very hard."

Police commander General Tanya Varela said authorities using drones saw that inmates in three pavilions were armed with guns and explosives and were trying to enter pavilion 2, which was without its leader who had been released earlier this week.

She said police officers entered to try to protect the pavilion and get the inmates in the other areas to return to their cells.

"These events are due to the dispute among criminal gangs over territory; there are now pavilions without leaders," she said.

The Attorney General's Office, on its Twitter account, raised the death toll to 68 and said 25 other inmates were injured.

The prison violence comes amid a state of emergency decreed by President Guillermo Lasso in October that empowers security forces to fight drug trafficking and other crimes.

On Saturday, Lasso tweeted that "the first right that we should guarantee should be the right to life and liberty, which isn't possible if security forces can't act to protect".

He was referring the Constitutional Court's recent refusal to allow the military into prisons despite the state of emergency.

Soldiers are currently outside the Litoral as well as relatives of inmates waiting for news of their loved ones.

"Enough of this. When will they stop the killing? This is a prison not a slaughterhouse, they are human beings," said Francisca Chancay, 55, whose brother has been in the prison for eight months.

Some were calling for Ecuador's security forces to take control of the prisons.

"What is (President) Lasso waiting for? That there are more deaths?," said Maritza Vera, 62, whose son is an inmate.

"Have mercy, where are the human rights. We thought this was going to change but it's worse."

Ecuador has about 40,000 inmates in its penitentiary system, which has a capacity to hold about 30,000.

Of this total, 15,00 inmates have not been sentenced.

Arosemena said authorities in Ecuador will deal with the prison overcrowding by granting pardons, relocating inmates and transferring some foreign inmates back to their homelands.

"There will be more than 1000 pardons, but this is part of a process," he said.

Australian Associated Press