The Dutch national Rijksmuseum announced the finding after a two-and-a-half-year research that used the most advanced imaging techniques and computer technology to map the 1642 masterpiece.
"It is fascinating to see Rembrandt searching for the right composition. We have discovered the genesis of The Night Watch," Taco Dibbits, the Amsterdam museum's director, said in a statement.
Scanning revealed many hidden details to the still of a Dutch militia group, including an extra sword and hat feathers that were eventually painted over.
The research is key to the work's long-term preservation, the museum said. It showed that some areas of the canvas were in poor repair, partly as a result of many treatments it had undergone since the 17th century.
The painting will be restretched next month to get rid of "ripples" in the upper left corner. These formed at the beginning of the 21st century when the painting was temporarily moved to another gallery and are attributed to temperature fluctuations.