The defence ministry plans to increase the number of aircraft equipped with airborne warning and control systems and install state-of-the-art radar to allow early detection of precision-guided missiles heading for Japan, the daily said.
It is also considering developing an advanced long-range surface-to-air missile, the report said, citing senior defence ministry sources.
The government has so far mainly focused on developing a ballistic missile defence system, primarily in response to a perceived threat from North Korea.
Meanwhile, China has equipped its fighter jets and submarines with domestically developed cruise missiles, which have a range in excess of 1,000 kilometers (625 miles), the newspaper said.
Beijing is also believed to have started developing advanced precision-guided missiles with a range of about 3,000 kilometers -- similar to that of the US military's Tomahawk cruise missile, it said.
Chinese fighter jets repeatedly approached Japan last year, coming close enough to launch a cruise missile before returning to Chinese air space, the newspaper said.
"We believe these acts were unlikely to be part of information-gathering exercises, but rather drills to prepare for a possible cruise missile attack on Japan," a senior Japanese defence official told the Yomiuri.