The man, who was suspected of being in the country illegally, began throwing fist-sized rocks at the agent from a hillside perch, the San Diego County Sheriff's Department said. The rocks became larger, and one of the bigger pieces hit the agent in the head.
The sheriff's department said the agent fired his gun at least twice Tuesday, fearing he might be killed or incapacitated if he was hit again in the head. The agent tried to revive the man, who died at the scene. The man's identity is unknown.
The agent, whose name was not disclosed, was treated at a hospital for minor injuries and released.
The episode in a remote, mountainous area about 4 miles east of San Diego's Otay Mesa border crossing comes amid debate about whether the Border Patrol should respond to rock attacks with lethal force.
Under current policy, agents can use deadly force if they have a reasonable belief that their lives or the lives of others are in danger. The Border Patrol has long maintained the rocks can be lethal weapons.
The incident began when two agents on foot separated Tuesday morning to arrest two people who were suspected of crossing the border illegally from Mexico, according to the sheriff's department, which is leading the investigation.
One agent saw a third person — also suspected of entering the country illegally — and ordered him to stop in English and Spanish, then chased him down a ravine and up a hill, where the shooting occurred, the department said in a press release that does not reveal sources of its account.
The Border Patrol said in a statement Tuesday that the agent feared for his life and that two people in the country illegally were arrested. Kelly Thornton, a spokeswoman for the U.S. attorney's office in San Diego, said prosecutors decided against charging them with a crime.
The Police Executive Research Forum, a nonprofit group that led a government-commissioned review, recommended that the Border Patrol and its parent agency, Customs and Border Protection, prohibit deadly force against rock-throwers and assailants in vehicles, Border Patrol Chief Mike Fisher told The Associated Press last year. Customs and Border Protection rejected the proposed curbs, which Fisher called "very restrictive."
Agents were attacked with rocks 339 times in the 2011 fiscal year, more than any other type of assault, according to the Department of Homeland Security inspector general. They responded with gunfire 33 times and with less-than-lethal force — a category that includes pepper spray and batons — 118 times.
Rock attacks fell to 185 instances in fiscal 2012, becoming the second-most-common type of assault. Agents fired guns 22 times and responded 42 times with less-than-lethal force.
A spokesman for the union representing Border Patrol agents said Tuesday that he was confident the investigation into the latest killing would find the agent did nothing wrong.
"The easiest way to stop these incidents from happening is to stop attacking Border Patrol agents," said Shawn Moran of the National Border Patrol Council.
Mitra Ebadolahi, an attorney for the American Civil Liberties Union of San Diego and Imperial counties, said there wasn't enough public information to say if the agent was justified but that the episode raised familiar questions about whether the Border Patrol can respond to rock attacks with nonlethal force.
She said she was troubled that there appeared to be no independent witnesses.
"It's imperative for the agency to behave honestly and transparently," Ebadolahi said.
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