Hegseth -- a former infantryman and Fox News personality -- was sworn in last weekend, having narrowly won Senate confirmation despite allegations of alcohol abuse, sexual misconduct and concerns over inexperience.
Key allies Japan and the United States are each other's top foreign investors, and 54,000 US military personnel are stationed in Japan, mostly in Okinawa east of Taiwan.
But President Donald Trump's "America First" approach could mean less cash from Washington for security in the region, analysts have warned.
"The Ministers affirmed their firm intent to continue the initiatives to reinforce the Alliance, including the upgrading of respective command and control framework and expansion of bilateral presence in the southwestern region of Japan," Tokyo's defence ministry said.
Nakatani said "he looks forward to working with Secretary Hegseth to further strengthen the Alliance capabilities to deter and respond amid the increasingly severe security environment" in the Asia-Pacific, the ministry statement added.
"The Ministers reaffirmed that Article V of the U.S.-Japan Treaty of Mutual Cooperation and Security applies to the Senkaku Islands," it said.
A chain of uninhabited islands claimed by Beijing but administered by Tokyo, known as the Senkaku in Japan and Diaoyu in China, have long been a point of tension between the neighbours.
Nakatani also extended his condolences to relatives of those killed in the recent air crash in the United States between a passenger jet and a military helicopter.
"The Ministers expressed their willingness to meet in person at the earliest possible time," it added.
On Saturday, Hegseth pledged to "restore the warrior ethos" in the Pentagon, thanking Trump for selecting him and Vice President JD Vance for his tie-breaking vote in the Senate that allowed his nomination to pass.
Vance's vote Friday evening was only the second time in history a vice president had to intervene to save a cabinet nominee and came after three Republicans -- including former leader Mitch McConnell -- cast ballots against Hegseth.
Hegseth has a combative media personality, fierce loyalty and telegenic looks -- common hallmarks in Trump's entourage.
Japanese Prime Minister Shigeru Ishiba has expressed a wish to meet Trump in Washington, with local media reporting that February 7 is being eyed as a potential date.
Ishiba said last week that Tokyo must "continue to secure the US commitment to the region, to avoid a power vacuum leading to regional instability".
"As the balance of power in the region undergoes a historic change, we must deepen Japan-US cooperation further, in a concrete manner," he told parliament.
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