China considers the democratic island its territory, part of "one China", and says it is the most sensitive and important issue in its ties with the United States.
When a reporter asked Biden if the United States would defend Taiwan if it were attacked, the president answered: "Yes."
"That's the commitment we made," he said, during a joint news conference with the Japanese leader. "We agree with a one-China policy. We've signed on to it and all the intended agreements made from there. But the idea that, that it can be taken by force, just taken by force, is just not, is just not appropriate."
He added that it was his expectation that such an event would not happen or be attempted.
Following Biden's comments, a White House official said there were was no change in policy towards Taiwan.
The president's national security aides shifted in their seats and tilted their heads, studying Biden closely as he responded to the question on Taiwan. Several looked down as he made what appeared to be an unambiguous commitment to Taiwan's defence.
Biden made a similar comment about defending Taiwan in October. At that time, a White House spokesperson said Biden was not announcing any change in US policy and one analyst referred to the comment as a "gaffe".
The United States has long agreed that there is one China, including Taiwan, but it has adopted its "strategic ambiguity" on the question of whether it would get involved in military conflict over the island.
The remarks came as Biden made tough comments about China's increasingly assertive posture in the region, saying he hoped Russian president Vladimir Putin would pay a price for his invasion of Ukraine in part to show China what it would face if it were to invade Taiwan.
The comments are likely to both infuriate Beijing and overshadow the centrepiece of Biden's Japan visit, the launch of an Indo-Pacific Economic Framework, a broad plan providing an economic pillar for US engagement with Asia.
His trip includes meetings with the leaders of Japan, India and Australia, in the "Quad" group of countries.
Japan's Kishida emphasised Tokyo's readiness to take a more robust defence posture, something the United States has long welcomed.
Kishida said that he told Biden that Japan would consider various options to boost its defence capabilities, including the ability to retaliate, signalling a potential shift in Japan's defence policy.
That would include a "considerable increase" in its defence budget, Kishida said.
"A strong Japan, and a strong US-Japan alliance, is a force for good in the region," Biden said at the news conference following their discussions.
Kishida said that he had gained support from Biden on Japan's becoming a permanent member of the UN Security Council amid growing calls for reform of the council. China and Russia are permanent members.
Worries are growing in Asia about an increasingly assertive China, particularly in light of its close ties to Russia, and tension has risen over self-ruled Taiwan, which China considers a renegade province.