The Environment Ministry began Thursday netting nonnative fish in the Ushigafuchi moat at the Imperial Palace to protect the native species there.
The first attempt, shortly after 9 a.m., found six nonnative bluegill and about 30 native "motsugo," a carp species.
The operation is being conducted by the Japan Wildlife Research Center and the Tokyo University of Fisheries, under a ministry commission.
The contents of the stomachs of the nonnative fish will be checked to see if they have been consuming native fish, the ministry said.
The native fish will be released into other moats.
The Ushigafuchi moat, one of 13 surrounding the palace, was drained Monday to 40 cm from the usual 1 meter to facilitate the operation. The ministry cleaned the 16,000-sq.-meter moat Tuesday and Wednesday because bicycles and other refuse in the water formed obstacles to the nets.
The palace moats have been home to a variety of native fish since the Edo Period. But in recent years, bluegill and black bass, introduced by anglers, have been dominant.