It's the first suicide in decades at the landmark site, Monsignor Patrick Jacquin, the cathedral's rector, told The Associated Press.
"It's unfortunate, it's dramatic, it's shocking," Jacquin said. The motives for the suicide, and the contents of the man's letter, were unclear.
In a message on her Twitter account, French far-right politician Marine Le Pen named the victim as a far-right author and historian. Police officials could not be reached to confirm the identification.
Police ushered people out of the cathedral after the shooting, Interior Minister Manuel Valls told reporters from the grand stone plaza in front of Notre Dame. "We call for compassion," he said.
It's highly unusual for the cathedral, visited by some 13 million people from around the world every year, to be evacuated.
Police, the Paris prosecutor and church employees gathered inside the cathedral, while puzzled tourists crowded outside on the island in the Seine River that has been home to the cathedral since the 12th century.
School groups lined up in hopes of entering the cathedral Tuesday evening, when it was expected to reopen for an evening service that church officials said would include a prayer for the man who committed suicide and other struggling souls.
Tuesday's death comes less than a week after another unusual suicide in central Paris, when a man shot himself in front of a dozen schoolchildren at a private Catholic school in the French capital.
Jacquin said a few people had committed suicide by jumping from Notre Dame's twin towers, but he had no knowledge of anyone ever committing suicide on the altar. The Eiffel Tower occasionally shuts down because of suicides or attempts to jump off its ledges.