The agency said it could spend several days at the site, which is about 100 miles from Tucson. The FBI and the Cochise County Sheriff's Office, which was also investigating, declined to say whether investigators have recovered guns or bullet casings.
No arrests have been made, but authorities suspected that more than one person fired at the agents. Agents and deputies are searching the area on ATVs, horseback and on foot with up to four helicopters overhead in the southern foothills of the Mule Mountains, which is considered a known smuggling area.
Nicholas Ivie, 30, and his partner were on patrol near the U.S.-Mexico border at about 2 a.m. Tuesday, when they were shot. Ivie did not survive. His body was flown to Tucson as investigators try and track down those responsible.
The agents were fired upon in a rugged hilly area about five miles north of the border as they responded to an alarm that was triggered on a motion sensor - one of thousands along the border that, when tripped, alert dispatchers that they should sent agents to a particular location. Authorities say it wasn't immediately known whether the agents returned fire.
Ivie is the third agent to die in the line of duty this year. Ivie lived in Sierra Vista with his wife and their two young daughters. The Border Patrol said Ivie worked for the agency since January 2008 and grew up in Provo, Utah.
His colleague, who was shot in the ankle and buttocks, was released from the hospital Wednesday. His identity was not released.
ABC News and The Associated Press contributed to this report.