Families are seeking news on loved ones but with some victims decapitated or dismembered, identifying the bodies could take days.
The gang-related violence is the worst in Ecuador’s history.
What is happening inside the Guayas prison complex, also known as the Litoral Penitentiary, is unclear.
Officials said on Wednesday the jail was back under their control, but early on Thursday neighbours said they had heard explosions and gunshots.
Shortly afterwards, police said it was sending 400 officers back in to “maintain order”.
Police commander Tannya Varela told Reuters the death toll could rise as security forces work their way through the jail.
“We have not yet completed the intervention in the penitentiary, so it is possible that there are other bodies inside, and some of the injured could die from their wounds,” she said.
How did the violence unfold?
The fight first broke out on Tuesday when inmates from one wing of the prison crawled through a hole to gain access to a different wing, where they attacked rival gang members.
Police managed to get six cooks, who were trapped in the wing where the fight happened, to safety and only two police officers were injured.
Ecuador’s prison director, Bolívar Garzón, said that police had entered the prison on Tuesday and found 24 bodies.
According to Mr Garzón, there was renewed shooting inside the prison overnight Tuesday into Wednesday and as police went through the prison wings one by one, they found scores more bodies, bringing the death toll to 116.
With security forces inside and outside of the jail, families of inmates face an anxious wait.
Some of the relatives said they had been sent photos and video from inside the prison but had been given no official confirmation as to whether their family member was among the victims.
Newspaper El Comercio reported that one woman had recognised her husband in one of the videos. She said he was one of those who had been decapitated.
When Ecuador’s President Guillermo Lasso announced that the death toll had risen to 116 from the initial 24, dozens of families rushed to the forensic laboratory where the bodies of the victims are being taken. They want to find out where their loved ones are and if they are still alive.
They have yet to get an answer and their anxiety only increased as explosions could again be heard coming from Guayaquil’s biggest prison, a sign that the gang war inside – said to be linked to the drugs trade – had not been brought under control.
Among them is Zenaida Moreira, 50, whose 23-year-old son was sent to the prison two years ago for stealing chairs from a school.
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Ms Moreira fears the worst after having seen videos of the carnage inside the jail.
I don’t know if one of the bodies I saw was his. I saw a decapitated head, the face is similar to his, but the authorities are not saying anything.
Her son would call her over from a phone smuggled into the prison but it has been days since she last heard from him.
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Her daughter María, Darwin’s 30-year-old sister, tried to reassure her. The women have heard that security personnel carried out a sweep of the prison on Wednesday and they hope that he only lost contact because his phone was seized.
But they are staying put outside the morgue, just in case.
The forensic lab is not the only place where relatives are gathering. The authorities have asked them to go to the Abel Jiménez sports stadium, where they have been promised updates and psychological support.
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