Chief Woodrow Kusse, head of the Pentagon Force Protection Agency, said there were multiple injuries in an exchange of gunfire at a public bus stop but declined to say if anyone was killed.
Kusse declined to speculate on the motive or to say whether the assailant was in custody but added that authorities were not actively looking for one.
He said the FBI was assisting in the investigation.
Warner said he was saddened to learn about a Pentagon police officer being killed on Tuesday "in a senseless act of violence."
The building was briefly put on lockdown as police responded to the incident.