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The agreement would facilitate the transfer of defense hardware and technology from Japan to Thailand, which has one of the region's biggest and most equipped armies and a long history of ties with the United States military.
"This will help improve national defense and support investment from Japan in this activity which is an important goal for Thailand," Thai Prime Minister Prayuth Chan-ocha said in a joint statement read alongside Kishida.
Prayuth said he discussed improvements in supply chains and the drafting of a five-year economic partnership with Japan, Thailand's biggest investor.
Southeast Asia has for decades been an important region for Japan, hosting some of its biggest names in industry, from infrastructure, engineering and industrial zones to the manufacturing of vehicles and electronics.
The region remains a battleground between the United States, Japan's close ally, and rival China, Southeast Asia's biggest trade partner. On his three-day trip Kishida also visited Vietnam and Indonesia, where Japanese firms maintain a large presence.
Nine Southeast Asian countries backed a United Nations resolution in March condemning the invasion, however, and Kishida thanked Prayuth for Thailand's support.
"I agreed with Prime Minister Prayuth that in any region the violation of sovereignty and territorial integrity, or unilateral changes to the status quo with force, should not be tolerated," he said.
Noriyuki Shikata, Japan's Cabinet secretary for public affairs, earlier on Monday told reporters that Tokyo would be extending a 50 billion yen ($385 million) loan to support Thailand's Covid-19 mitigation efforts.