The Chinese J-15 fighter jets directed their radar at Japanese F-15 aircraft in separate incidents on Saturday.
"These radar illumination went beyond what is necessary for the safe flight of aircraft," Japan's Defence Minister Shinjiro Koizumi said in a post on X.
Japan, he said, had lodged a protest with China over the "regrettable" incident.
A fire-control radar lock is one of the most threatening acts a military aircraft can take because it signals a potential attack, forcing the targeted aircraft to take evasive action.
The encounters near islands close to territory claimed by both Japan and China are the most serious run-ins between the two militaries in years and are likely to further escalate tension between the neighbours.
Relations have already soured after Prime Minister Sanae Takaichi warned that Japan could respond to any Chinese military action against Taiwan if it also threatened Japan's security.
Democratically governed Taiwan is claimed by Beijing and lies just 110km from Japan's westernmost Yonaguni Island.
Japan hosts the biggest overseas concentration of US military power, including warships, aircraft and troops, with a big chunk of that contingent, including thousands of US Marines based in Okinawa.
The Chinese J-15 jets involved in the two incidents were launched from China's Liaoning aircraft carrier, which was manoeuvring south of the Okinawan islands along with three missile destroyers, Japan said.
In past close military encounters between the two countries, Japan said a Chinese warship locked its radar on one of its destroyers in the East China Sea in 2013. In 2016, Beijing accused Japanese jets of directing their fire-control radar on Chinese fighters.
In June, Chinese jets reportedly flew dangerously close to a Japanese patrol aircraft near Okinawa.
On Thursday, China was deploying a large number of naval and coast guard ships across East Asian waters, which at one point numbered more than 100, Reuters reported citing sources and intelligence reports.
Taiwan's government described that build-up as posing a threat to the Indo-Pacific region. Japan said it was monitoring Chinese activity closely.
