The troops began patrolling the capital of Tegucigalpa and the city of San Pedro Sula on Friday.
Lobo says the soldiers will coordinate with police to patrol neighborhoods that are hotspots for crime. He says 800 soldiers have been assigned to Tegucigalpa and 600 to San Pedro Sula.
National Police Director Juan Bonilla says this is part of a "frontal attack against crime."
According to Honduras' National Autonomous University, the Central American nation recorded 7,173 homicides in 2012 and 7,014 in 2011. Honduras has 8 million people.