The probe by the Department of Homeland Security's Office of Inspector General involves a review of accusations of brutality and excessive force as it works to determine whether reforms have been implemented.
The review, briefly referenced in a 100-page report released this month, was launched after 16 members of Congress expressed concern over the 2010 death of an unarmed Mexican migrant in San Diego. They asked the Department of Homeland Security to determine whether the incident is "emblematic of a broader cultural problem" within the agency.
"It is ongoing," Arlen Morales, a spokeswoman for the Inspector General's Office, said Thursday.
She declined to comment on details of the investigation or when it began, but noted it could take up to a year to complete.
U.S. Customs and Border Protection also would not comment, saying only that it fully cooperates with the Inspector General's Office, agency spokesman Michael Friel said.
In the San Diego shooting, Anastasio Hernandez, 42, died in May 2010 after being shot with a stun gun by a Border Patrol agent at the San Ysidro port of entry. An autopsy found he died of a heart attack, with a heart condition and methamphetamine listed as contributing factors.
The coroner's report, citing a San Diego police detective, said Hernandez was agitated and confrontational after he was detained by agents while crossing the border illegally and became violent when his handcuffs were removed.
Eugene Iredale, an attorney for the man's family, told the Associated Press in July the U.S. Justice Department's civil rights division was presenting evidence to a grand jury in the case amid signs that prosecutors were considering criminal charges.
The Justice Department has declined to comment, only noting the case remains under investigation.
It is extremely rare for border authorities to face criminal charges for deaths or injuries to migrants. In April, federal prosecutors said there was insufficient evidence to pursue charges against a Border Patrol agent in the 2010 shooting death of a 15-year-old Mexican in Texas.
The Border Patrol considers the use of deadly force against rock-throwers generally acceptable, noting the projectiles can be deadly, but critics of the practice claim it's an unfair fight.