The measurement of photosynthetic activity using the chlorophyll fluorescence is used widely from the photochemical experiment level to the field level such as the monitoring of canopy photosynthesis and the remote sensing, because it enables a non-destructive measurement in a short period. However, there is one problem in the method, which is the uncertainty of the depth of signal detection in the leaves of higher plants. In this method, a measurement light is illuminated to the upper surface of leaves and the fluorescence can be detected from the surface. However, there is a light intensity gradient inside a leaf, which is caused by the light absorption by chloroplasts. Depending on the depth of the chloroplasts, the light intensity and the photosynthetic activity can be changed, which results in an error of the estimation of photosynthetic activity. In the present study, the chlorophyll fluorescence was measured in each depth of the leaves, using a micro thin optical fiber and a micro-manipulator, and the photosynthetic activity of the whole leaf was estimated. Leaf mass per area and chlorophyll content were aimed at as the traits, which can be correlated with the extent of the error. The method of the error correction using the relationships between these two traits and the extent of the error will be discussed.