U-1206 was one of the late war boats fitted with the new deepwater high-pressure toilets which allowed them to be used while running at depth. Flushing these toilets was extremely complicated and special technicians were trained to operate them.

On April 14, 1945, 8 miles off Peterhead, Scotland, while cruising at a depth of 200 feet, misuse of the new head caused large amounts of water to flood the boat. According to the Commander's official report, while in the engine room helping to repair one of the diesel engines, he was informed that a malfunction involving the toilet caused a leak in the forward section. The leak flooded the submarine's batteries (located beneath the toilet) causing them to release chlorine gas, leaving him with no alternative than to surface. Once surfaced, U-1206 was discovered and bombed by British patrols, forcing Schlitt to scuttle the submarine. One man died in the attack, three men drowned in the heavy seas after abandoning the vessel and 46 were captured.[2] Schlitt recorded the location as 57°24′N 01°37′W / 57.4°N 1.617°W / 57.4; -1.617 but the wreck could not be relocated.