Economic security, particuarly in relation to China, was also a key topic.
The EU will lift restrictions on farm and fish imports from Japan imposed following the Fukushima nuclear accident in 2011.
According to European Commission President Ursula von der Leyen, the decision has been made based on recent scientific evidence.
The measures, imposed over 12 years ago now, stopped agriculture and fish products from Fukushima entering Europe, after the nuclear plant meltdown contaminated the region.
Von der Leyen's announcement came on Thursday after the 29th EU-Japan summit in Brussels, where Japanese Prime Minister, Fumio Kishida, met with her and European Council President Charles Michel.
"We agreed to lift the remaining restrictive import measures that were linked to the Fukushima accident," the Commission president told reporters.
"We have taken this decision based on science and based on the proof of evidence and based on the assessment of the International Atomic Energy Agency and we also agreed to solve several other trade issues in the course of this year, in particular the access for our agricultural products to the Japanese market."
Leaders also discussed China's recently announced decision to impose curbs on exports of gallium and germanium. The two materials are used in computer chips, solar panels and other crucial products.
Beijing wants to take the fight to the collective West, which has stepped up its own restrictive measures on China, including on the export of high-tech semiconductors.
Some experts argue it will not have the impact China wants, but regardless, Brussels and Tokyo said on Thursday that they will increase their own cooperation to counter Beijing's influence.
"We shall continue closely towards maintaining and strengthening a free and open international order based on the rule of law which again we reaffirmed at today’s meeting," the Japanese Prime minister said.
"Especially as we face a severe security environment, we welcome a stronger engagement by the EU in the Indo-Pacific."
Both sides agreed to work together to find alternate sources of critical raw materials used in what are considered crucial products. Beijing has a near monopoly in this field and the EU and Japan want this over-reliance to end.