The Topeka Capital-Journal reported the Shawnee County Sheriff's Office identified the slain officers as Cpl. David Gogian, 50, and officer Jeff Atherly, 29.
Authorities were looking for a suspect, identified as David Edward Tiscareno of Topeka, who was described as armed and dangerous, the newspaper said.
The shooting occurred after officers were dispatched to Dillons supermarket on a report of a suspicious vehicle.
"Within a couple of minutes, one of the officers reported that shots were fired," Kristen Veverka, police spokeswoman said.
City police Lt. Ron Gish said the two officers who were shot were in separate vehicles. He said a third officer was uninjured.
Police, acting on a tip received after the shooting incident, set up a perimeter around a city residence.
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