The outline, which will be sent to local authorities, provides guidance on how to evacuate in the event of a biochemical attack and how to disseminate emergency information.
Japan has been threatened by Islamic militants opposed to its ground-breaking deployment in Iraq. Tension is also rising with North Korea, whose firing of a missile over Japan in 1998 prompted Tokyo and Washington to work on a missile defence shield.
The manual was drafted in accordance with legislation enacted in June to let Japan's military cooperate with the United States in the event of a local or regional armed conflict.
The legislation has been criticised as a departure from Japan's post-World War II pacifism. Last Friday, the government revised its basic defence policy to partially lift a three-decades-old ban on military exports.
The evacuation guidelines advise that in the event of a nuclear, biological or chemical attack, residents should "avoid moving in a downwind direction and wear gloves, goggles, rain coats and other items to reduce the exposure of skin."
It takes a short period of time for a ballistic missile to land in Japan, "making it imperative to localise damage through swift dissemination of information and appropriate counter-action," the draft manual said.
The manual will be finalised in March after input from local administrators.
The evacuation law passed in June provided for the government to appropriate private property for public use and limit media broadcasts in an emergency.
The draft manual said that restrictions on individual rights should be limited to the "minimum possible" and that "special consideration" should be given to freedom of speech by broadcasters.
About 550 Japanese troops are on a non-combat, humanitarian mission in southern Iraq on Japan's first military deployment since 1945 to a country where there is active fighting.