Billed as one of Japan's biggest defence export deals since World War II, Australia will pay US$6 billion (Aus$10 billion) over the next 10 years to acquire the fleet of stealth frigates.
Australia is in the midst of a major military restructure, bolstering its navy with long-range firepower in an effort to deter China.
It is striving to expand its fleet of major warships from 11 to 26 over the next decade.
"This is clearly the biggest defence-industry agreement that has ever been struck between Japan and Australia," Marles said, touting the deal.
"This decision was made based on what was the best capability for Australia," he added.
"We do have a very close strategic alignment with Japan."
Mitsubishi Heavy Industries was awarded the tender over Germany's ThyssenKrupp Marine Systems.
Mogami-class warships are advanced stealth frigates equipped with a potent array of weapons.
Marles said they would replace Australia's ageing fleet of Anzac-class vessels, with the first Mogami-class ship to be on the water by 2030.
"The Mogami-class frigate is the best frigate for Australia," said Marles.
"It is a next-generation vessel. It is stealthy. It has 32 vertical launch cells capable of launching long-range missiles."
The deal further cements a burgeoning security partnership between Australia and Japan.
Japan is deepening cooperation with US allies in the Asia-Pacific region that, like Tokyo, are involved in territorial disputes with China.
Both Japan and Australia are members of the "Quad" group alongside India and the United States.
Japanese government spokesman Yoshimasa Hayashi said Tuesday the deal was "proof of trust in our nation's high-level technology and the importance of interoperability between Japan's self defence forces and the Australian military."
It was also a "big step toward elevating the national security cooperation with Australia, which is our special strategic partner", Hayashi told reporters in Tokyo.
- 'More lethal' -
Japan's pacifist constitution restricts it from exporting weapons -- but Tokyo has in recent years loosened arms export controls to boost sales abroad.
"This is Japan's largest defence export deal since 1945 with a non-US partner," said Yee Kuang Heng from the University of Tokyo's Security Studies Unit.
"And only the second since Tokyo loosened its guidelines on defence exports in 2014, which led to exports of air surveillance radar to the Philippines."
Heng said the deal was a "massive shot in the arm" for Japan as it sought to strengthen its defence manufacturing industry.
Australian defence industry minister Pat Conroy said the Mogami-class frigates were capable of launching long-range Tomahawk cruise missiles.
"The acquisition of these stealth frigates will make our navy a bigger navy, and a more lethal navy," he said.
The first three Mogami-class frigates will be built overseas, Conroy said, with shipbuilding yards in Western Australia expected to produce the rest.
Australia announced a deal to acquire US-designed nuclear-powered submarines in 2021, scrapping a years-long plan to develop non-nuclear subs from France.
Under the tripartite AUKUS pact with the United States and the United Kingdom, the Australian navy plans to acquire at least three Virginia-class submarines within 15 years.
The AUKUS submarine programme alone could cost the country up to US$235 billion over the next 30 years, according to Australian government forecasts, a price tag that has stoked criticism.
Major defence projects in Australia have long suffered from cost overruns, government U-turns, policy changes and project plans that make more sense for local job creation than defence.
Australia plans to gradually increase its defence spending to 2.4 percent of gross domestic product -- above the 2 percent target set by its NATO allies, but well short of US demands for 3.5 percent.
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