Cho's trip was the first to Japan by a sitting Taiwanese premier since 1972, except for a typhoon-enforced stopover by Yu Shyi-kun in 2004, Japan's foreign ministry told AFP.
The trip follows a sharp deterioration in Japan-China relations.
Chinese foreign ministry spokesman Guo Jiakun said Cho had "evil intentions, surreptitiously and sneakily going to Japan to conduct separatist provocative petty acts".
"Such underhand dealings and tricks are despicable," he said at a regular news conference on Monday.
"Japan's tolerance for provocation and wanton behaviour will definitely come at a price, and all consequences resulting from this must be borne by Japan."
Cho was reportedly accompanied by Taiwan's representative to Japan and the island's sports minister.
"There was no contact with Japanese government officials," Japanese government spokesman Minoru Kihara told reporters.
"We are aware of the reports, and as we are aware that the Taiwanese side is explaining it was a private one (visit), the government is not in a position to comment," Kihara said.
Back in Taiwan, Cho said Sunday it was a "holiday and a day off".
"The trip was self-funded and it was a private activity. The only arrangement was to cheer for Team Taiwan together with our fellow citizens. There was no other purpose, so there are no further comments," Cho said.
The current spat with China was sparked by Prime Minister Sanae Takaichi suggesting in November that Japan might intervene militarily in any Chinese attempt to take Taiwan.
China regards the democratic island as part of its territory and has not ruled out force to annex it.
burs-aph/mtp
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