Hegseth also stopped short of publicly calling on Tokyo to hike military spending, saying in Japan he trusted the close US ally to "make the correct determination of what capabilities are needed".
"America is committed to sustaining robust, ready and credible deterrence in the Indo-Pacific, including across the Taiwan Strait," Hegseth said, using Washington's term for the Asia-Pacific region.
Beijing has stepped up military pressure in recent years around Taiwan, including near-daily air incursions, and has not ruled out using force to bring the self-ruled island under its control.
US President Donald Trump's "America First" approach could mean weakening the US commitment for security in the region, analysts have warned.
But Hegseth said the previous US administration had "created this vacuum, a perception that America was not strong, and wasn't prepared to deter conflicts from starting".
"Our job now at this moment, here with our allies, is to say: We are re-establishing deterrence. Peace through strength, with America in the lead, is back," the Pentagon chief told reporters.
He said Washington would "build an alliance so robust that both the reality and the perception of deterrence is real and ongoing, so that the Communist Chinese don't take the aggressive actions that some have contemplated they will".
- 'Who makes these deals?' -
Hegseth, 44, a former infantryman and Fox News personality, hailed the "extraordinary strength of America's alliance with Japan".
"President Trump has also made it very clear, and we reiterate, we are going to put America first. But America first does not mean America alone," he said.
"America and Japan stand firmly together in the face of aggressive and coercive actions by the Communist Chinese."
There have also been expectations that, as he has done in Europe, Trump would press its allies in Asia to increase military spending and to do more to ensure their own defence.
"We have a great relationship with Japan. But we have an interesting deal with Japan that we have to protect them, but they don't have to protect us," Trump said this month.
"I actually ask, who makes these deals?"
Japan's government has also been reeling from Trump's decision to impose a 25 percent tariff on auto imports from April 3.
The United States has 54,000 US military personnel stationed in Japan, mostly in Okinawa, east of Taiwan.
Hegseth said he "did not talk specific numbers" about defence spending in his talks with Japanese counterpart Gen Nakatani on Sunday.
"We're confident that Japan will make the correct determination of what capabilities are needed inside our alliance to make sure we are standing shoulder to shoulder," he said.
"They have been a model ally and we have no doubt that will continue. But we also both recognise everybody needs to do more."
Nakatani said he told Hegseth that spending should be "implemented based on Japan's own judgement and responsibility".
"I also explained Japan has continuously been working on a drastic strengthening of our defence capability... on which we received understanding from the US side," he said.
- Counterstrike -
Japan has been shedding its strict pacifist stance, moving to obtain "counterstrike" capabilities and doubling military spending to the NATO standard of two percent of GDP.
Former US President Joe Biden and Fumio Kishida, Japan's prime minister at the time, announced a "new era" in cooperation at a summit at the White House last year.
This includes the creation of a new Japan-based US headquarters to take over operational oversight of US forces in Japan from US Indo-Pacific Command in Hawaii.
It will serve as a counterpart to Japan's new Joint Operations Command for all its armed forces, making the two militaries more nimble in the case of a crisis over Taiwan or the Korean peninsula.
"We will accelerate our efforts to improve inter-operability and conduct effective bilaterally joint activities across the spectrum from peacetime to contingency," Nakatani said on Sunday.
"Expansion of the Japan-US presence in (Japan's) southwestern region is one of our alliance's top priorities," he said.
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