Pfleger said he ordered the flag outside his church to be hung upside down, traditionally seen as a sign of distress, to serve as a symbol of the escalating problem of youth violence in Chicago, CNN said Friday.
"We're hiding it. We're ignoring it. We're denying the problems," he said, referring to the 36 children and teens killed in Chicago during the current school year.
The Chicago Sun-Times said the St. Sabina Church flag was torn down by an unidentified individual after Pfleger began his protest.
Pfleger, who heads the city's largest African-American Roman Catholic parish, said he replaced the flag Thursday and is determined to continue his protest even if similar actions occur in the future.
"There's more attention being given to the flag than to children dying," the priest said. "What do we care about children dying?"
"Life is at risk and particularly our children," he added regarding the trend of youth violence. "If it's a distress signal, we're feeling it in Chicago."