The flight was part of the Treaty on Open Skies, which allows military aircraft from the US and Russia and other nations to fly aerial observation flights to observe military sites of the 34 signatory nations, reports CNN.
The Russian Air Force Tupolev Tu-154 on Wednesday afternoon passed at around 3,700 feet over downtown Washington and the Joint Base Andrews in Maryland where Air Force One is based, according to tracking website Flightradar24.
The jet is authorised to enter P-56, the highly secure airspace surrounding the White House.
A law enforcement source told CNN that the plane also overflew Camp David, the Presidential retreat in the Catoctin Mountains, the Trump National Golf Course in Virginia and Mount Weather, one of the US government's secret relocation bunkers.
The Open Skies Treaty has been in effect since 2002.