Japanese Prime Minister Sanae Takaichi told parliament on Nov. 7 that use of force against the island could warrant a military response from Tokyo.
On Friday, Beijing said that it had summoned Japan's ambassador, while Tokyo said it had summoned China's ambassador after an "inappropriate" and now-removed online post.
Tokyo has since said its position on Taiwan, just 100 kilometers (62 miles) from the nearest Japanese island, is unchanged.
In an online post late Friday, China's embassy in Japan warned its citizens against traveling to the country.
"Recently, Japanese leaders have made blatantly provocative remarks regarding Taiwan, severely damaging the atmosphere for people-to-people exchanges," the WeChat post said.
The situation presents "significant risks to the personal safety and lives of Chinese citizens in Japan", it added.
"The Ministry of Foreign Affairs and the Chinese embassy and consulates in Japan solemnly remind Chinese citizens to avoid traveling to Japan in the near future."
Reacting to the statement, Japan's Chief Cabinet Secretary Minoru Kihara told reporters Saturday that Beijing's call was "inconsistent with the promotion of a strategic and mutually beneficial relationship", Jiji Press reported.
The Japanese government has requested the Chinese side to take "appropriate measures", Jiji reported.
In a further development Saturday, China's largest airlines offered full refunds for flights on Japan routes before the end of the year.
Air China, China Southern and China Eastern all published separate statements on the policies, which will allow ticket holders to refund or change Japan itineraries free of charge for flights from Saturday through Dec. 31.
China and Japan are key trading partners, but historical mistrust and friction over territorial rivalries and military spending often test those ties.
Takaichi, a conservative and China hawk, has toned down her rhetoric since assuming office last month.
But just weeks into her administration, the neighbors are at odds.
Addressing parliament on Nov. 7, Takaichi said that an armed attack on Taiwan could warrant sending troops to the island under "collective self-defense".
If an emergency in Taiwan entails "battleships and the use of force, then that could constitute a situation threatening the survival (of Japan), any way you slice it", she said.
Security legislation passed in 2015 allows Japan to exercise the right to "collective self-defense" under certain conditions including if there was a clear danger to the country's survival.
Strategic ambiguity
Despite the escalating diplomatic spat, Takaichi has indicated she has no intention of retracting her statement and insisted it was consistent with Tokyo's long-standing policy.
But she said she would refrain from referring to specific scenarios in the future.
Previous Japanese prime ministers have avoided commenting directly on Taiwan's defense, choosing instead to maintain so-called strategic ambiguity.
Japan lodged a protest over the since-removed social media post, and Takaichi's ruling party passed a resolution calling for the envoy to be declared persona non grata.
Before taking power, Takaichi, an acolyte of ex-premier Shinzo Abe, was a vocal critic of China and its military build-up in the Asia-Pacific.
Takaichi has visited Taiwan in the past and met Taipei's representative at a recent APEC summit, where she also held talks with Chinese President Xi Jinping.