"Siphoning hundreds of thousands of dollars from hard-working Border Patrol agents, many of whom put their lives on the line every day to protect this country, is a particularly troubling form of corruption that must be addressed," said Laura Duffy, the U.S. attorney in San Diego.
Bonner, 59, did not immediately respond to phone messages to his office and pager.
George McCubbin, who succeeded Bonner as union president, said the alleged corruption was limited to Bonner.
"Obviously this is going to be a black eye on our organization. For years we were always above any of this. It's clear this is an isolated incident," McCubbin told The Associated Press. "There are no other union officers involved. This is strictly on T.J."
McCubbin said the union's executive board learned about the investigation in April 2010. Bonner retired from the Border Patrol a month later after a 33-year career with the agency, and the union allowed him to continue serving as president until his two-year term expired in March 2011.
Bonner submitted six years' worth of travel expenses to the government at the end of 2009 and filed a grievance when the Border Patrol refused to pay, McCubbin said.
"The agency said this doesn't smell right, and that's when they started their investigation," he said.
The indictment says Bonner worked with an alleged conspirator who served as the union's secretary treasurer from 1978 to last year but does not name the person. Mark Conover, an assistant U.S. attorney, said the person has not been charged and declined to comment further on whether there are other targets.
Bonner, a San Diego-area resident widely known as T.J., has been a fixture on cable television and in congressional hearings. News reporters often turned to him for pithy quotes on border security issues even after he retired.
He was the union's voice at a time when the agency saw enormous growth to more than 20,000 agents and erected hundreds of miles of fencing and other barriers.