Poisons and drugs were used in secret shinobi missions. Different schools have different versions and uses. Some use venom extracted from puffer fish and some even use opium. Poisons could be used to poison water supplies and food.
The Shoninki shinobi manual mentions the use machin (まちん), which is a poison derived from strychnine tree seeds, which is fed to guard dogs to intoxicate them and dehydrate them to death. Although water will cure their dehydration which was countered by adding iron filings to their source of water to kill the guard dogs.
One of the organic poisons used was made from common fruit. Cyanide was extracted from a variety of sources, such as apple seeds, plum seeds, cherries seeds and many more. It was readily available to the shinobi and was used often.
Tomato and rhubarb leaves also held a poison. Eating the leaves cause cardiac problems, ultimately resulting in cardiac arrest.
The amanita phalloides is a deadly mushroom. The poison in the mushroom was 10 times more powerful than that of cyanide. Eating the mushroom was certain death, and it was easy to slip a piece of the mushroom in almost any meal.
The poison could be used in various ways, depending on the situation. For example, if the shinobi could slip it into the victims food while its being prepared without knowing what kind of danger he was in, the victim would eat the food infested with the poison. Not all the poisons used by the shinobi were fatal, some of them were used to merely paralyze or cause blindness. It was not always necessary to kill. Soft-cased bombs used by the shinobi were could also be used to release poison gas.
Another thing the shinobi did was dip their weapons, such as the shuriken in the poison. This was so when it punctured the skin of their target, the fast acting poison would take its course, causing much more devastating than the blade itself. Poison was never directly added to Katana or Wakizashi as it would increase mold growth around the blade, blunting and weakening the blade.