Marchanti's son Aaron is a city firefighter. Fire Chief James S. Clack ordered the flags lowered.
"We are one family," Baltimore Firefighters Union IAFF Local 734 said in an e-mail Tuesday. "This is the same honor we show a member who dies in the line of duty."
Marchanti and another officer were shot to death Saturday afternoon inside an Interior Ministry building in Kabul. The killings came amid rising Afghan fury over the burning of copies of the Quran and other Muslim holy books at a NATO base in the country.
The violent unrest is seen as a new challenge to the U.S. mission in Afghanistan, which centers on training Afghan security forces to protect the country's fragile central government after foreign troops leave in 2014.
President Barack Obama and NATO commander Gen. John R. Allen have apologized for the burning. Afghan President Hamid Karzai has appealed for calm.
Robert Marchanti, 48, of Gardenville, was a longtime physical education teacher in the Baltimore County public schools. He leaves his wife, Peggy, their four children and a grandchild.