The FBI said one explosive device was found inside the bunker and another was in the PVC pipe negotiators used to communicate with hostage-taker Jimmy Lee Dykes, ABC News reported.
Both devices were "disrupted," the FBI said, adding that the search for more hazards would go on through Wednesday on the property near Midland City.
The FBI said preliminary investigation reports indicate Dykes engaged in a firefight with SWAT agents before they stormed the bunker, killing the 65-year-old Vietnam veteran and rescuing the boy, identified as Ethan.
Agents used two explosions to gain entry to the bunker, which was reinforced to thwart an attempted entry by law enforcement, the FBI said.
ABC News said it learned Dykes fired first on the agents during the bunker raid. The agents returned fire, killing Dykes. Ethan was rescued.
The raid came six days after Dykes boarded a school bus, fatally shot bus driver Charles Poland Jr. and abducted the boy, who suffered no physical injuries.
Ethan was to celebrate his 6th birthday Wednesday.
Ethan's relatives told ABC's "Good Morning America" Tuesday the boy seemed as "normal as a child could be" after his experience.
"He's happy to be home," Ethan's great uncle Berlin Enfinger said. "He's very excited and he looks good."
CBS News reported security footage from the school bus reveals the exchange between Dykes and Poland unfolded over several minutes. Poland opened the emergency exit and told the children to run, but Ethan, who was in front of the bus, froze.
Minutes into the exchange, Dykes kills Poland for not cooperating and took Ethan to the bunker where they were holed up for several days.