TEHRAN, Young Journalists Club (YJC) -The victims appeared to have been killed by "asphyxiation," the Amazonas state government said in a statement, a day after 15 people were killed in one of the prisons.
Officials had initially put the number of the dead at 42, but later revised the number to 40 without explanation.
At least 25 of the victims were found in the Antonio Trindade Penal Institute near Manaus, the capital of Amazonas, where all four prisons are located.
The federal government has dispatched reinforcements to boost security in the jails.
"I just spoke with (Justice) Minister Sergio Moro, who is sending a prison intervention team to Amazonas so that he can help us in this moment of crisis," state Governor Wilson Lima said.
An investigation launched into Sunday's mass killing at the Anisio Jobim Penal Complex has been widened to include Monday's deaths.
Four of those killed in the latest violence were found at the Anisio Jobim jail, which was also the scene of a prison rebellion that lasted almost 20 hours and left 56 people dead in January 2017.
Another five were killed at the Provisional Detention Center for Men and six died at the Puraquequara Prison Unit.
Outbreaks of deadly violence continue to happen in Brazil's jails due to the lack of "structural changes," according to experts.
"Prisons continue to be places of serious violations of human rights," Juliana Melo, a professor at the Federal University of Rio Grande do Norte and expert on Brazil's prisons, told AFP.
"The conditions are appalling, with a majority of prisoners poor, black, badly schooled and marginalized."
"Intense disputes" between criminal factions for control inside and outside the prisons fuel the violence, she added.
Brazil has the world's third largest prison population after the United States and China, with 726,712 inmates as of June 2016, according to official statistics.
The population is double the capacity of the nation's jails, which in the same year was estimated to be 368,049 inmates.
The federal government had been expected to add another 115,000 inmates by the end of 2018, Human Rights Watch said in a recent report.
"Overcrowding and understaffing make it impossible for prison authorities to maintain control within many prisons, leaving detainees vulnerable to violence and recruitment into gangs," it said.
Along with severe overcrowding and gang violence, riots and breakout attempts in Brazil's prisons are not uncommon.
"Deaths in Brazil's prison system are shamefully recurrent," said Julita Lemgruber, a former director of Rio de Janeiro's penitentiary system and professor at Candido Mendes University.
"They are recurrent because those who die are originally from the poorest sections of the population and are people who are not clear about their rights and who do not pressure the state to be compensated for those deaths."
Sunday's clashes at the Anisio Jobim Penal Complex broke out around 11:00 am (1500 GMT) during visiting hours at the facility.
"It was a fight between the inmates. There had never been deaths during the visits," Colonel Marcos Vinicius Almeida told reporters.
Some of the inmates were stabbed with sharpened toothbrushes, Almeida said.
He emphasized that authorities had reacted within minutes to the violence, preventing a potentially worse result.
But urgent measures were needed to stop the never-ending cycle of violence, said Lemgruber.
"A short-term strategy is to hold the federal government and state governments accountable," she said.
"The lives of those inside are the responsibility of the state and the state must pay for it."