The legislation, which was criticized by the opposition, must still be given the green light by the upper house, where its passage is nearly certain as Prime Minister Junichiro Koizumi's coalition also enjoys a majority.
The bill was drafted amid worry that Japan would waste time in administrative procedures before reacting to an attack, as a missile fired from North Korea would reach the country in 10 minutes.
North Korea provoked an international outcry in 1998 by firing a missile over Japan, in what the Stalinist state claimed was a satellite launch. On May 1, it launched a short-range missile into the Sea of Japan amid a standoff over its nuclear ambitions.
The main opposition Democratic Party of Japan opposed the bill, saying that parliament needed to be notified before a missile intercept. The legislation passed with an amendment that the government would explain any intercept afterward to parliament.
Japan is barred from using force or maintaining a military under its constitution imposed by the United States after World War II.