Saturday's raid was a bold strike against Tijuana's former mayor, who has prospered through decades of never-proven suspicion that his family's fortunes are linked to illegal drugs.
Troops found 40 rifles, 48 handguns, 9,298 bullets, 70 ammunition clips and a gas grenade, authorities said.
Mexican law limits ownership of large-caliber firearms to the military and requires licensing of most other guns. Violations can be punished by as long as 15 years in prison in some cases.
Hank Rhon, 55, was flown to Mexico City and officials said he was being investigated by a division specializing in organized crime. Ten others were also in custody with Hank Rhon.
The former mayor wrote in a a hand-written account to human rights officials that he was awakened early Saturday by masked men and military personnel who burst into his bedroom and did not show a search warrant. The men took photographs of him standing next to weapons that he says he had never seen before, the letter states. Authorities did not let him call his lawyer until the afternoon, says the letter, released Sunday by Hank Rhon's spokesman, Francisco Ramirez.
"They held me in the 'lobby' with my forehead to the wall, so I could not see what these people were doing in my home," Hank Rhon said in the letter, which was his first public statement since his detention.
"They took me to the station of the Attorney General's Office, where I am being held without knowing why they detained me," the letter added.
His wife, Maria Elvia Amaya de Hank, said that after arresting several of Hank Rhon's security guards, the soldiers told her they were recovering arms intended solely for military use.
Amaya de Hank insisted all the weapons in the house had permits and demanded that her husband be released.
"I am fully confident that our authorities will quickly resolve the painful affair and do it with transparency, for my husband has been incommunicado until now," she said in a statement Saturday.
Amaya de Hank was hospitalized after the army raid, said her press secretary, Martina Martinez.
The federal Attorney General's Office said the troops staged the raid after three armed people detained near a hotel told them that weapons were hidden in the compound, which Hank Rhon's spokesman said includes the home, a casino, the ex-mayor's private zoo, a soccer complex and a school.
Heriberto Garcia, Baja California's human rights ombudsman, said Hank Rhon told him that armed men in hoods, some in civilian garb and others in military uniform, broke into the house and disarmed his security guards.
Hank Rhon was mayor of Tijuana from 2004 to 2007, but lost in a run for Baja California state governor that year. He is a self-proclaimed billionaire who owns a dog track, a nationwide chain of off-track betting parlors and the Tijuana soccer team that last month won advancement into Mexico's top soccer league.
His supporters charged that the arrest was an effort to tarnish his once-dominant Institutional Revolutionary Party, or PRI, ahead of Mexico's 2012 presidential election and the 2013 vote for Baja California governor. Hank Rhon has been widely considered a potential candidate to try again to wrest the governor's office from President Felipe Calderon's National Action Party.
"They want to finish off his chances in the election," said Edgar Velasquez, a 23-year-old dance teacher who wore a red T-shirt from Hank Rhon's failed 2007 campaign and was among a crowd of about 200 protesters outside the federal Attorney General's Office after the arrest.
But the PRI's president, Humberto Moreira, said he saw no evidence of a strike against his party. "I don't think it is part of a witch hunt," he told reporters in the central city of San Luis Potosi.
Hank Rhon is the son of a legendary figure in the PRI, Carlos Hank Gonzalez, who served in Mexico's Cabinet, was governor of Mexico state and later was mayor of Mexico City. He started his career as a school teacher and died a billionaire in 2001 after a life in public service.
Hank Rohn's elder brother, Carlos Hank Rhon, sold Texas-based Laredo National Bancshares in 2004, three years after he and another bank he controlled agreed to pay $40 million to settle a dispute with the U.S. Federal Reserve over ownership rules.