The National Human Rights Commission, a government-funded agency with independent powers, denied the maps - similar to a comic-style guide booklet Mexico distributed last year - would encourage illegal immigration.
Officials said the maps would help to guide those in trouble to rescue beacons and areas with mobile phone reception.
The maps will also show the distance a person can walk in the desert in a single day.
Mauricio Farah, one of the commission's national inspectors, said: "We are not trying in any way to encourage or promote migration.
"The only thing we are trying to do is warn them of the risks they face and where to get water, so they don't die."
Russ Knocke, a spokesman for the US Homeland Security Department, questioned whether the maps would keep those crossing the border safer.
"It is not helpful for anyone, no matter how well intended they might be, to produce road maps that lead aliens into the desolate and dangerous areas along the border, and potentially invite criminal activity, human exploitation and personal risk," he said.
Some advocates of greater immigration control were irritated by the announcement.
Mark Krikorian, executive director of the Centre for Immigration Studies, a Washington-based thinktank, said: "What's next? Are they going to buy them bus tickets to Chicago?
"It is clearly a bad thing for Mexico to be encouraging illegal immigration."
The comic booklet for migrants was distributed by the government in early 2005 and warned of the perils of crossing illegally into the US, while offering tips to stay safe.
"It is not helpful for anyone, no matter how well intended they might be, to produce road maps that lead aliens into the desolate and dangerous areas along the border, and potentially invite criminal activity, human exploitation and personal risk"
Russ Knocke, US Homeland Security Department
The booklet, of which about 1.5 million were printed, enraged some advocates of stricter immigration policies in the United States who argue that it encouraged illegal migration.
Farah said his commission was trying to prevent death and estimated that about 500 Mexicans died trying to cross the border in 2005. Many die in the desert, where summer temperatures soar above 38C, and many drown while crossing the Rio Grande river.
The commission plans to hang the poster-size maps in March in places where migrants will see them, such as migrant-aid groups, the commission's offices and in Mexican border towns.
They were designed by the rights group Humane Borders, based in Tucson, Arizona, which operates some of the desert water stations. The group previously distributed about 100 posters in the Mexican border town of Sasabe.
The Reverend Robin Hoover, president of Humane Borders, said maps were needed in southern Mexico so migrants could weigh the risks before leaving home.
Some of the posters have warnings, such as: "Don't go. There isn't enough water," but officials conceded many migrants were unlikely to heed the advice.
Knocke said the US had increased personnel and surveillance along the border to discourage immigrant smugglers and immigrants themselves.
"Our message should be clear: We are securing our borders and we're dramatically increasing the likelihood of apprehensions," he said.
Mexicans in the US are a huge
source of revenue for Mexico
Farah said migration "is a human right" and that "the United States should be grateful" the commission is doing something to curb the toll, because "hundreds of thousands of Mexicans help maintain their economy".
Mexicans working in the US are a huge source of revenue for Mexico, sending home more than $16 billion in remittances in 2004, Mexico's second largest source of foreign currency after oil exports according to the country's central bank.
Dollars for Brincos
Last year Argentinian artist Judi Werthein created a "crossing trainer" for illegal Mexian immigrants.
The shoe, named a Brinco, contained a compass, flashlight and painkillers.
Part of an art project, the footwear also carried a symbol of Aztec culture and American culture - the American eagle. The trainers were given free to immigrants but were later sold at a fashionable boutique in San Diego for $215 a pair.