The air force were scrambled to three regions near Okinawa, Japan’s defence ministry revealed.
The alert came when Chinese H-6 bombers flew towards their neighbour’s boundary.
Officials revealed it is the first time the bombers have flown between Okinawa’s main island and Miyako Island.
While not a violation of the Japanese airspace, the ministry described the incident as a provaction and Tokyo defence minister Itsunori Onodera has raised the issue with Beijing.
He told reporters: “It was the first time we have recorded Chinese military aircraft flying this route.
“We expressed our concern through diplomatic channels.”
A spokesman for the defence ministry said the bombers may have been gathering intelligence.
It comes as Japan holds drills ahead of North Korea’s provocations and ballistic missile tests.
China has kept a distance from the crisis, apart from promising to reduce trade to the hermit state.
North Korea has increased efforts to produce parts for a new nuclear reactor it is building while continuing to operate the main existing one that provides fuel for its atom bombs, the UN nuclear watchdog has said in an annual report on Friday.