He added: “We have to protect Taiwan as a democratic country.”
In response to the deputy defence minister’s comments, Wang Webin, a spokesperson for China’s foreign ministry condemned the remarks as “a serious violation”.
“We deplore the erroneous remarks by the senior official of the Japanese government, and we have lodged solemn representations,” he said.
“This is highly sinister, dangerous and irresponsible.
“This politician also openly called Taiwan a country, in serious violation of the China-Japan joint statement.”
Japan recognised Beijing’s authority over Taiwan in 1972 but in recent years has begun reneging on its commitments to China.
Japanese ministers now fear that if anything were to happen in Taiwan, several other contested islands in the region might also be affected.
Several Japanese islands are in close proximity to China, such as Okinawa, the Senkaku and Ryukyu islands.
Back in 2013, Beijing claimed the Ryukyus belonged to China however, Japan vehemently rejected the notion.
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Mr Suga said all three “countries” had taken stricter measures against the spread of the Coronavirus pandemic.
Beijing also protested the Prime Minister’s remarks, saying Mr Suga “broke Japan’s long-standing promise not to regard Taiwan as a country.”