The official said Johnson has been reviewing the rules about when border agents can use their guns since he took office in December.
The official was not authorized to publicly discuss internal deliberations and spoke on the condition of anonymity.
Customs and Border Protection, which oversees the Border Patrol, has been criticized by civil rights groups and others for allowing border agents to use deadly force against people blamed for throwing rocks at them.
Border Patrol Chief Michael Fisher said last year that a report by the Police Executive Research Forum, a group that led a government-commissioned review, recommended a ban on deadly force against rock throwers and assailants in vehicles. CBP rejected the recommendations, which Fisher described to The Associated Press as "very restrictive." Now, agents can use deadly force if they have a reasonable belief that their lives or the lives of others are in danger.
The Los Angeles Times reported Thursday that it obtained a copy of the report, which it described as critical of the Border Patrol's "lack of diligence" in investigating agents who fired their guns.
The report found agents sometimes put themselves in harm's way by remaining close to rock throwers when they could have moved away, according to a person who read it and spoke to the AP on condition of anonymity because it has not been publicly released. It said agents may have been partly motivated by frustration in some rock-throwing cases.
The 21-page review of incidents from January 2010 to October 2012 raised questions about cases in which agents fired across the border fence into Mexico and said "too many" cases don't meet the threshold for use of deadly force, the person said.
Rep. Zoe Lofgren, a California Democrat, said she read the report and found it "very disturbing."
"It makes clear that there needs to be very serious reform efforts at the agency," she said. "You don't use lethal force against nonlethal force."
The Homeland Security official said Johnson's review was not prompted by any additional incidents or new details.
CBP's policies have been criticized by some civil rights groups and questioned by others.
"When a young person throws a rock across the border ... some agents respond with a gun and others don't seem to respond at all," U.S. Sen. Robert Menendez, a New Jersey Democrat, said at a congressional hearing in January. "There seems to some need for consistency in the response to these incidents."
The Border Patrol has long maintained that rocks are lethal weapons.
According to the Homeland Security inspector general, agents were attacked with rocks 339 times in the 2011 budget year. Rock-throwing incidents were the most common assault reported. Agents responded with gunfire 33 times and with less-than-lethal force 118 times.
The latest incident happened on Feb. 18, when an agent fatally shot Jesus Flores Cruz, 41, who allegedly struck the agent in the head with a rock near San Diego. The Border Patrol said Agent Daniel Basinger feared for his life.
Associated Press reporter Elliot Spagat in San Diego contributed to this report.