China's steady expansion of its military and economic influence in Asia Pacific has also encouraged Japan and Australia to draw closer militarily.
The 2 leaders also discussed bilateral cooperation to achieve Abe's "free and open Indo-Pacific strategy", and confirmed their close cooperation with the U.S. and India.
Mr Turnbull and Mr Abe will give a joint press statement on Thursday evening.
Japan and Australia share a vision for the Indo-Pacific region as the Australian government cites the key phrase of a "stable and prosperous Indo-Pacific" as a main pillar in its Foreign Policy White Paper, released last year for the first time in 14 years.
Canberra has also been at odds with Beijing over an Australian minister's criticism of Chinese aid pouring into Pacific island nations, arguing it has created "useless buildings".
Turnbull told reporters the visit was a reminder of the big threats in the region, "terrorism on the one hand, and, of course, the reckless regime in North Korea on the other".
North and South Korea held rare talks in a border village this week where they agreed to form their first unified Olympic team, in women's ice hockey, and have their athletes parade together during the opening ceremony of next month's Winter Olympics in South Korea.
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Official Skopje also said that the right conditions exist to move forward with process of finding a solution to the name issue.
Abe and Turnbull agreed that safety in Asia can not be achieved without a nuclear-free Korean Peninsula.
In January past year, the two countries reached a revised acquisition and cross-servicing agreement, which allows them to provide ammunition, water, food and other supplies to each other.
He also attended a special session of Japan's national security council, spoke to business leaders and had dinner with Abe before leaving Japan.
During his one-day trip, Australian Prime Minister Malcolm Turnbull visited a military training base outside Tokyo, viewed a Patriot Advanced Capability-3 missile interceptor and climbed on board an Australia-made armoured vehicle used in Japan. The two leaders are to discuss deepening security ties, including a potential permanent security partnership.
"Abe and I are personally committed to having this deal signed and sealed by March", Turnbull said in a speech in Tokyo. The pact had been cast into doubt after President Donald Trump pulled the US out. The 11 members agreed on "core elements" of the deal in November when they met in Vietnam.
"North Korea presents and unprecedented imminent threat", Abe said during a joint news announcement with Turnbull. The agreement will set the legal status for the movement of military personnel, equipment and weapons between Australia and Japan.
The new pact would be the first of its kind for Japan, which has a Status of Forces Agreement that governs the USA troops permanently stationed in the country, but which does not envisage Japanese troops visiting the US.