EU foreign policy chief Josep Borrell will meet his Japanese counterpart Takeshi Iwaya, who told reporters this week that the pact comes "as Japan and the EU face an increasingly challenging security environment".
He did not mention China, but Japan has previously called its neighbour its greatest security challenge as Beijing builds up military capacity in the region.
After the Tokyo talks, Borrell will head to South Korea, where concerns about North Korea will top the agenda.
The United States has said thousands of North Korean troops are in Russia readying to fight in Ukraine.
Pyongyang also test-fired one of its newest and most powerful missiles on Thursday, demonstrating its threat to the US mainland days ahead of elections.
"My visit to two of our closest partners in the Indo-Pacific is a key milestone in our efforts over the past five years to strengthen the EU's active engagement," Borrell said in a statement Thursday.
"We have secured alignment on geopolitical issues and advanced the values we share," he said, promising "a new chapter in our ever-closer relations".
The Japan-EU Security and Defense Partnership, expected to be announced on Friday, "aims to further develop, deepen and strengthen cooperation and dialogue in all areas of security and defense," Iwaya said on Tuesday.
"Specifically, we envision cooperation in the areas of maritime security, space, cybersecurity, and hybrid threats, including foreign disinformation and interference," he said.
The security of the Asia-Pacific region is "inseparable from that of Europe and the Atlantic", Iwaya added.
Japan is ramping up defence spending to the NATO standard of two percent of GDP by 2027, partly to counter China, which is increasing military pressure on Taiwan.
Beijing claims the self-ruled island as part of its territory and has not ruled out using force to bring it under its control.
Japanese Prime Minister Shigeru Ishiba, who could head a minority government after a disastrous general election last week, has said that "today's Ukraine could be tomorrow's East Asia".
Ishiba has also called for the creation of a NATO-like regional alliance with its tenet of collective security, although he has conceded this will "not happen overnight".
The same warning was issued by Ishiba's predecessor Fumio Kishida, who was hosted by US President Joe Biden for a state visit in April at which the allies announced plans to boost their defence partnership.
Japan, which for decades has relied on the United States for military hardware, is also developing a new fighter jet with EU member Italy and Britain set to be airborne by 2035.
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