Now embarrassed border officials say the mistake could cost the federal government more than $3 million to fix.
The barrier was part of more than 15 miles of border fence built in 2000, stretching from the town of Columbus to an onion farm and cattle ranch.
A U.S. Customs and Border Protection spokesman said the vertical metal tubes were sunk into the ground and filled with cement along what officials firmly believed was the border. But a routine aerial survey in March revealed that the barrier protrudes into Mexico by 1 to 6 feet.
James Johnson, whose onion farm is in the disputed area, said he thinks his forefathers may have started the confusion in the 19th century by placing a barbed-wire fence south of the border. No one discovered their error, and crews erecting the barrier may have used that fence as a guideline.
"It was a mistake made in the 1800s," Johnson said. "It is very difficult to make a straight line between two points in rugged and mountainous areas that are about two miles apart."
The Mexican government was notified and did what any landowner would do: They sent a note politely insisting that Mexico get its land back.
"Our country will continue insisting for the removal (of the fence) to be done as quickly as possible," the Foreign Relations Department said in a diplomatic missive to Washington.
When the barrier was built in 2000, the project was believed to cost about $500,000 a mile. Estimates to uproot and replace it range from $2.5 million to $3.5 million.
Michael Friel, the spokesman for Customs and Border Protection, said the barrier was "built on what was known to be the international boundary at the time." He acknowledged the method used was "less precise than it is today."
The International Boundary and Water Commission, a joint Mexican-American group that administers the 2,000-mile border, said the border has never changed and is marked every few miles by tall concrete or metal markers.
Sally Spener, a commission spokeswoman in El Paso, said the agency is generally consulted for construction projects to ensure that treaties are followed. The commission is working with the Department of Homeland Security "to develop a standardized protocol" for building fences and barriers.
"We just want to make sure those things are clear now," Spener said.
New Mexico Sen. Jeff Bingaman asked Customs and Border Protection officials to build a new fence on U.S. soil before the old one is torn down.
Bingaman said he was concerned about security issues in Las Chepas, the small Mexican village where most area residents live. New Mexico once sought permission to raze the community because it was known as a popular staging area for illegal immigrants and drug smugglers.
Back at his farm, Johnson said he doesn't understand why the placement of the barriers has become an issue now since his family's fence went unquestioned for more than a century.
"The markers are in the right place, and the fence is crooked," Johnson said. "But for 120-plus years it was agreed upon that that fence was the border."