The police service tweeted Thursday that about 400 police officers were engaged in an operation to restore order "and guarantee security in the prison complex."
On Wednesday, at least two officers were injured when rioting inmates, armed with guns, attacked police sent in to retake control of the facility.
Soldiers and tanks are also stationed outside the jail, where hundreds of worried family members have gathered, desperate for news from the men locked up inside.
"It is a very painful thing," said Juana Pinto, who is seeking news about her inmate son.
"For us family members, this is a horrible thing... We do not know what to do. We feel powerless, not to be able to help them," added Cecilia Quiroz, a relative of another prisoner.
Tuesday's violence was the latest in a series of bloody prison clashes that have claimed the lives of more than 200 inmates in Ecuador so far this year.
At least six of the victims were beheaded, according to the national prosecutor's office.
Ecuador's prison system has 65 facilities designed for about 30,000 inmates but a population of 39,000, watched over by 1,500 guards, a shortfall of about 3,000, according to experts.
Corruption is rife and inmates are able to acquire arms and ammunition.
On 23 February, simultaneous riots at four jails including Guayaquil left 79 inmates dead, several of them also beheaded.
Last week, police confiscated two pistols, a revolver, some 500 rounds of ammunition, a hand grenade, several knives, two sticks of dynamite and homemade explosives at one of the city's prisons.
Two weeks ago, Guayaquil's Prison Number 4 was attacked by drones, part of "a war between international cartels," prison authorities said. There were no casualties in that attack.
'Collapsed' prison system
The country's human rights ombudsman said there were 103 killings in prisons in 2020.
Criminal groups "have taken over the country's prisons and are trying to send a message to the state that they are stronger than the rule of law," said Itania Villarreal, a former director of the agency in charge of prisoner rehabilitation.
"The prison system has collapsed," she said.
In response to the latest riot, the government decreed a state of emergency allowing it to suspend prisoners' civil rights and to use public force to restore order.
Security expert Freddy Rivera of the Latin American Faculty of Social Sciences in Quito said many prisoners had ties not only to Mexican cartels, but also to gangs in neighboring Colombia.
Ecuador's prisons have become "criminal central command centes" from which criminal activities are planned and ordered, he told AFP.
Located between Colombia and Peru, the world's leading cocaine producers, Ecuador is a key transit for drug shipments to the United States and Europe.
Guayaquil is Ecuador's most populous city and its main port.