But officials stressed late Thursday that they had not yet found any bodies or even confirmed a shootout happened.
Interior Minister Mauricio Lopez Bonilla told The Associated Press that police and soldiers would begin searching on foot and in the air at first light Friday, looking for the scene of the reported gunfight in Peten province near the border with Mexico.
Authorities initially said Thursday night that they were investigating whether Guzman was one of at least two men killed in the remote area, but hours later backtracked and said they had only received reports of a battle from local people.
Government spokesman Francisco Cuevas first told Guatevision Television that two drug gangs had clashed in Peten, an area that has seen an increase in drug violence and that at least two men had died in the shootout.
"We have to wait for all the technical information in order to determine if, in fact, one of the dead is of Joaquin 'El Chapo' Guzman," Cuevas said.
Later, Cuevas told Mexico's Televisa network that authorities hadn't yet found a body or the scene where reports said a shootout took place.
He never said what led officials to think that one of the dead men might be Guzman.
But Interior Department spokeswoman Carla Herrera told The Associated Press that one of the victims physically resembled the drug lord. She said officials had asked the Mexican government to send Guzman's fingerprints to compare them to the man found inside a vehicle and to send investigators.
However, Herrera's boss, Lopez Bonilla, told the AP that it was residents of the town of San Francisco who had told officials of a gunbattle and reported that one of the people killed looked like Guzman.
"The fact is we don't have any of this information confirmed," Lopez Bonilla said.
Mexican President Enrique Pena Nieto said late Thursday that he had no information on the case.
"I don't have any information that can confirm that," he told reporters.
Peten province is an isolated area of jungle and ranches where 27 ranch workers were massacred in 2011 by the Zetas drug gang, a top rival for Guzman's Sinaloa drug cartel.
Guzman, who has been in hiding since escaping from a Mexican prison in a laundry cart in 2001, is one of the world's most dangerous and most wanted fugitives.
He's also one of the richest: Forbes magazine has estimated his fortune at $1 billion.