Planes are taking off from Australian airports to keep watch on the Sea Shepherd Conservation Society's vessel, the Steve Irwin.
Flights from Western Australia have located the Steve Irwin but others from Hobart failed to find the ship, Fairfax newspapers reported on Wednesday.
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The federal opposition and Greens leader Bob Brown have demanded the government ban the use of Australian airports for the spy flights.
"Instead of Australia sending a surveillance vessel to watch the whalers, the Japanese are using Australian soil to watch the whale defenders," Senator Brown said.
"It's totally back to front."
Garrett calls for restraint on issue
The Hobart flights were paid for by Wellington-based Omeka Communications, a PR company engaged by Japan's Institute of Cetacean Research, air industry sources told Fairfax.
Omeka principal Glenn Inwood, who is the spokesman for the institute, and another man were aboard flights from Hobart, a source said.
Pilots said surveillance flights from Albany in WA had cost a "truckload" of money.
Sea Shepherd leader Paul Watson said his ship was circled by an aircraft on December 9 just outside Australia's 200-nautical-mile exclusive economic zone south of Albany.
Within hours, a Japanese whale chaser ship latched on to the Steve Irwin, enabling the fleet to track the vessel's movements, he said.
A spokesman for Environment Minister Peter Garrett did not respond to questions but again called for restraint on all sides and said the government was engaged in an "unprecedented" diplomatic effort on the issue.
