An All Nippon Airways flight from Shanghai made an evasive manoeuvre while approaching Haneda airport around 6am (4am Thailand time) on Tuesday, the company said.
ANA Flight NH968's collision avoidance system was activated as the plane neared the airport in Tokyo.
The pilot followed the system's instruction and climbed to avoid another aircraft.
The Ministry of Land, Infrastructure, Transport and Tourism said its inspection plane, which had taken off from Runway D, was flying nearby and that the details were being investigated.
None of the 197 passengers and crew were injured and no problems were found with the aircraft, according to ANA.
