The former internal affairs chief at Customs and Border Protection claims the agency has routinely tried to cover up deadly shootings.
In an interview with the Center for Investigative Reporting, James Tomsheck said at least a quarter of the nearly 30 deaths involving Border Patrol agents could be described as "highly suspect."
Since 2010, 170 Customs and Border Protection employees, including Border Patrol agents, have been arrested on corruption-related charges since 2004, according to the report.
One high-profile case occurred in San Diego when two brothers who were employed as U.S. Border Patrol agents were convicted of smuggling undocumented immigrants into the U.S. from Mexico using their official Border Patrol vehicles between 2005 and 2006.
In 2013, Raul and Fidel Villareal were sentenced to serve 35 and 30 years in prison, respectively.
In the article, Tomsheck estimates 5 to 10 percent of the men and women employed by the agency are "actively corrupt or were at some point in their career."
Tomsheck also reportedly alleges that agents claim undocumented immigrants hurt or killed in agent-involved shootings were on U.S. soil when they were not.
The death of a man in San Ysidro, California is still unresolved four years later. A witness videotaped the encounter between Anastasio Rojas and Border Patrol agents in 2010.
Officials said Rojas was uncooperative and defiant as agents took him to the border for deportation and the use of force was justified.
Rojas' family has filed a wrongful death suit and is demanding agents get more training and wear body cameras.
In March, the agency issued new guidelines prohibiting agents from shooting at moving cars or people throwing rocks unless there is a direct threat.
An audit showed Border Patrol agents would unnecessarily step in front of fleeing cars to justify firing at passengers, NBC News reported.
However, union representatives have argued the number of assaults on Border Patrol agents while on the job have increased. In 2012, the number of incidents reported jumped 70 percent over those the year prior.
In the article, Tomsheck also said that in the post 9/11 expansion, the agency hired people not fit to wear a badge.
NBC 7 reached out to a representative for the Border Patrol agents' union about Tomsheck's allegations and has yet to receive a response.
In a written statement, Southern Border Communities Coalition (SBCC) Director Christian Ramírez said that the agency has begun a process to be more transparent but adds, “The administration must take immediate steps to ensure that CBP is held accountable and effective oversight mechanisms are implemented.”
The Southern Border Communities Coalition (SBCC), is made up of the San Diego Immigrant Rights Consortium (CA), Border Action Network (AZ), Arizona Sonora Border Coalition (AZ), Taskforce for Immigrant Advocacy & Services (NM) and Rio Grande Valley Equal Voice Network (TX).