The Trade and Industry Ministry is promoting specialty toilet paper for emergency use, marking Monday's national disaster prevention day.
Officials say people immediately think of food and water as relief goods, but easily forget toilet paper, and get desperate when it's too late.
Government and industry officials said 41% of the country's toilet paper supply comes from Shizuoka, central Japan, one of Japan's most earthquake-prone areas.
Toshiyuki Hashimoto, a ministry official in charge of paper products, warned of a nationwide toilet paper shortage crisis for about a month if the area is hit by an imminent Tokai mega-quake, a lesson learned from the deadly March 2011 earthquake and tsunami in northern Japan.
Lack of toilet paper could even cause further discomfort when people start using tissue paper, which is not water soluble and could clog up toilets.
Japan takes disaster preparedness serious, and even more so since three years ago, when about 19,000 people were killed in the tsunami-hit northern coast.
Hundreds of thousands of Japanese take part in an annual drill every Sept 1 - the anniversary of the 1923 Great Kanto Earthquake in Tokyo that killed more than 140,000 people. Led by the prime minister, the exercise also involves the military and civilians.