Wednesday's riot was the second deadly melee in four days at the prison just across the U.S. border from San Diego.
Thirteen prisoners were shot to death and four others died from injuries sustained in the melee, said Rommel Moreno, the attorney general of Mexico's Baja California state. Officials initially reported 19 inmates died, but Moreno said that figure was mistaken. He said 45 people were injured, including prisoners, guards and police.
Blaming prison troublemakers for the uprisings that killed a total of 21 inmates, state authorities immediately transferred 250 inmates to other prisons in Tecate and Ensenada.
But relatives of the inmates say they rioted again because they were not given food or water since Sunday.
Francisco Javier Sanchez, the state's human rights ombudsman, said the riot Wednesday began in the women's section of the prison after they were served spoiled eggs for lunch and given no water.
Sanchez said human rights workers counted 166 injured inmates from Sunday's uprising, some with gunshot wounds, multiple bone fractures and bruises.
He said authorities failed to address the prisoners' complaints and "thought the situation was under control but it wasn't."
He said 80 percent of the prison was destroyed, although other officials said the destruction was not that widespread.
After waiting days outside the prison, families started receiving word Thursday on the fate of their loved ones. About a dozen government workers sat at a long table in a shaded parking area near the prison, checking lists of names.
Mike Apodaca, 55, of San Diego, said he has been waiting since Monday morning for news on his son, Michael John Apodaca, 25, who was charged with drug possession about four months ago. He was relieved to learn that his son's name was not on any list of dead or injured, although authorities had not accounted for his whereabouts.
"I'm worried," he said, choking up. "I want to know where he is."
Apodaca's son is one of 256 U.S. citizens jailed at La Mesa.
Two American inmates were wounded - one of them shot in the face
said Charles Smith, a spokesman at the U.S. Consulate in Tijuana. Smith said the consulate was trying confirm a prison official's report that an American was among the dead.
Apodaca said his son told him he shares a six-person cell with about 30 other men in the overcrowded prison.
"He said they got roaches that bite them all the time," he said. "They got rats as big as cats."
The earlier riot erupted Sunday after a guard killed a 19-year-old inmate, said Augustin Perez, the spokesman for the state Public Safety Department. The inmate had confronted three guards after they found drugs and cell phones in his prison cell. One of the guards was arrested and the other two are being sought, Perez said.
State investigators suspended La Mesa's warden and two other top prison officials pending an investigation of irregular conduct. Perez said he did not have details of the allegations and that such investigations are routine after a riot.
La Mesa has long been held up as the quintessential example of what's wrong with Mexico's corrupt and overcrowded prison system. Its inmates gained worldwide notoriety after they built and ran their own city inside the penitentiary's sprawling courtyard, buying and selling townhomes, running shops and hiring prostitutes.
Federal police bulldozed the village in 2002 under former President Vicente Fox, who touted its destruction as proof his government was serious about combatting corruption. But the overcrowded prison has held onto its reputation for violence and ungovernability.
The prison was built to hold 4,000 inmates but currently holds 8,100, said Daniel de la Rosa, the state public safety secretary.