These places are called yorishiro, and they are visibly marked with shimenawa rice straw ropes, which besides indicating a sacred place are also protecting them against evil spirits. Photographed here is one such yorishiro, a sacred tree (shinboku) of the Wakamiya Inari Shrine in Nagasaki.
EXIF info:
Nikon Df
Lens: 24-70mm F/2.8G
Focal Length: 24mm
Aperture: F/13
Shutter Speed: 1/60s
ISO Sensitivity: ISO 4000