The white flags were removed by noon, but police said they are investigating the issue, which may indicate a serious security breach on one of the city's most secured landmarks.
One of the white flags, viewed via video, appeared to have faint traces of stars and stripes on it. Police said it was not clear what time they were placed there - or by whom, but told Fox News that there is a chance the flags were put in place legally.
"Why are there white flags on top of the Brooklyn Bridge?"
A Twitter handle named @BicycleLobby claimed responsibility Tuesday, tweeting, "Earlier today we hoisted two white flags to signal our complete surrender of the Brooklyn Bridge bicycle path to pedestrians."
The Twitter handle later claimed to be a parody site and distanced itself from the tweet.
Either way, it appeared to take city leaders by surprise.
Mark S. Weprin, a city councilman, posted a photo of the white flag on his Twitteraccount. He wrote, "Why are there white flags on top of the Brooklyn Bridge?"
Brooklyn Borough President Eric Adams told The New York Post that security for these high-risk targets are a top priority for law enforcement.
"Political and social expression, whatever its message may be, has a place in our society, but not at the expense of others' security. I am confident in the NYPD's ability to investigate this matter," he told the paper.
A city employee told NBC 4 that the flags are 12 feet by 18 feet.
The iconic span connects Manhattan to Brooklyn and is close to police headquarters near City Hall.
The city's Department of Transportation, which operates the bridge, referred all queries to the NYPD.
