Australian and Japanese fighter jets will participate in joint war games this year, as the two countries ramp up defence ties.
Malcolm Turnbull wrapped up his whirlwind 16-hour visit to Tokyo on Thursday night attending a special dinner at the residence of Japanese Prime Minister Shinzo Abe.
The North Korea nuclear threat and China's rise loomed large during their bilateral meeting.
The official communique stressed the importance of buddying up with India and the US as part of efforts to revive a four-country security forum, which is widely seen as an effort to counter China's growing influence.
At a defence base outside of Tokyo, the two leaders inspected Japan's Patriot missile defence system which protects the Tokyo skyline from North Korean rockets.
North Korea launched two ballistic missiles over Japan last year.
Mr Turnbull insisted new found North and South Korean unity ahead of the Winter Olympics in PyeongChang was nice but it won't denuclearise the Korean Peninsula.
"We have to be very clear-eyed about this," he said.
"History tells us a very bitter lesson about North Korea. They have a long habit of ratcheting up their militarisation and then ... going into a lull for a while trying to persuade people that they're changing their ways, changing nothing and then ratcheting up again."
Mr Abe characterised North Korea's actions as an "unprecedented and imminent threat" and called for "pressure to be maximised by all possible means".
The two leaders are seeking closer defence ties and in 2018 are expected to sign an agreement spelling out the legal status of joint military exercises.
Under the deal, Japanese troops could conduct military exercises out of Darwin - almost 76 years since Japan's air force bombed the city in World War II.
After catching a ride in a Chinook helicopter in the morning, Mr Turnbull indulged his love of public transport aboard a crowded Japanese subway train in the afternoon.
Mr Turnbull reflected on his and Mr Abe's efforts to keep the "train moving" on the Trans-Pacific Partnership trade pact, which was thrust into limbo when President Donald Trump withdrew the US.
The pair are optimistic a wayward Canada can be corralled back to the table and the agreement can be finalised by March when trade ministers from 11 countries meet in Chile.
