Japan last week asked Taiwan if it could fly over all of Taiwan's westernmost island of Yonaguni, but the Foreign Ministry said no.
US officials had given part of the airspace over Yonaguni to Taiwan after World War II, and Taiwan uses the east coast of the island to conduct sensitive military activities.
Japan communicated its request "inadequately" to Taiwan, which wants to keep its existing air space intact, the foreign ministry said in a statement.
"If they are upset, too bad, unless they go to Washington and kick us around," said Alexander Huang, strategic studies professor at Tamkang University in Taipei. "We listen to Washington, but not Tokyo."
The snub will further chill once close but informal Taipei-Tokyo relations that have become more distant since Taiwan President Ma Ying-jeou took office in 2008 and courted stronger ties with China.
Japan and Taiwan also dispute the eight uninhabited East China Sea islands known as the Senkakus, which are rich in fisheries and possibly undersea natural gas reserves. The issue flared in 2008, when a Taiwan fishing boat collided with a Japanese coastguard vessel and sank.
