The army helicopter crashed around 11:00 am (0800 GMT) during a training flight, the governorate said in a statement, adding that one military personnel was injured.
The governor's office said "there was no information to indicate that any civilian was injured" after the accident in Sancaktepe district on the province's Asian side.
The helicopter hit a four-storey building, state news agency Anadolu reported, with images published showing the destroyed helicopter close to residential apartments.
Turkish Defence Minister Hulusi Akar was at the scene and told reporters that the injured soldier was in intensive care.
"Our heroic pilots tried to make an emergency landing for a reason we do not yet know and as you can see, they showed great effort to ensure they did so without hurting anyone," Akar told reporters, quoted by CNN Turk broadcaster.
The Istanbul public prosecutor launched an investigation into the crash, Anadolu said.
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