On Wednesday, the Chinese foreign ministry excluded a reporter from the Sankei Shimbun -- a Japanese conservative daily critical of China -- from a media pool covering the start of a meeting between China's Foreign Minister Wang Yi and Japanese vice foreign minister Takeo Akiba.
Other Japanese media covering the event in Beijing then boycotted the pool coverage in protest.
Japan's top government spokesman Yoshihide Suga confirmed Tokyo had lodged a protest with China over the incident.
"The Japanese government believes that respect for basic human rights including freedom of expression is a universal value in the international community, and ensuring those rights is important in any country," Suga told reporters in Tokyo.
But Chinese foreign ministry spokesperson Hua Chunying dismissed the criticism, saying Beijing had been "wrongfully accused".
"The Japanese government needs to rein in its own journalists," she told reporters.
"They should ensure that their media respects their host country, follows the rules... so as to enhance mutual trust and understanding between the two countries, instead of doing the opposite, this is common sense."
Akiba, who was in Beijing ahead of Prime Minister Shinzo Abe's visit to China expected in October, also protested to his Chinese opposite number Le Yucheng, Suga said.
Suga however said bilateral relations between the two regional rivals are improving.
"The date of Prime Minister Abe's visit is under coordination right now," Suga said, adding that "we hope to push up to a new stage the relationship between Japan and China through visits by high level officials."
Fumihiko Iguchi, executive officer of the Sankei Shimbun, described Beijing's actions as "unfair obstruction of legal newsgathering activities that cannot be ignored."
"We express our regret," he said in a Wednesday statement, adding that the daily "will do our best to continue giving our readers accurate information about the situation in China".