The white flags - international symbols of surrender - fluttered Tuesday from poles on the stone supports that hold cables above the bridge connecting Brooklyn and Manhattan.
One of the flags appeared to have faint traces of stars and stripes on it and NYPD officers said the white flags may have been painted over American flags.
Police said it isn't clear what time the white flags were placed there - or by whom.
Several officers scaled the bridge and lowered the flags on the Manhattan side around 11 a.m. as traffic inched along the bridge.
The bridge is one of the most heavily secured landmarks in the city, constantly monitored by surveillance cameras.
Police said they would review surveillance cameras to determine how the flags were apparently switched.