The area is on a shipment route for drugs brought from Colombia to the US and Guatemalan officials said they had shut down border crossings with El Salvador and Honduras to prevent the attackers from fleeing the country.
Trejo said police arrested three Mexicans and three Guatemalans who were carrying automatic rifles and grenades near the shootout.
Investigators were trying to determine if those arrested were linked to the attack.
Trejo said more than 100 police officers were sent to the area to set up roadblocks and to guard the six men who were arrested.