The Chinese jet, supposedly a Y-9 type reconnaissance plane, entered the South Korean air defence identification zone, dubbed KADIZ, at around 10:21 a.m. local time (01:21 GMT) and left it half an hour later, the agency reported, citing the South Korean Joint Chiefs of Staff.
Then the jet returned to KADIZ at around 11:54 local time to leave it three hours later after flying along the South Korean east coast.
Later in the day, the South Korean Defence Ministry tasked a military attache working in the Chinese Embassy in Seoul with filing a motion of protest and calling on China to prevent similar situations from recurring.
South Korean military officials believe that the move was aimed at testing Seoul's response.
A section of KADIZ overlaps with Chinese and Japanese air defence zones, which is a source of potential regional tensions.