Discussing the economic relations between the two countries, the two officials underlined the importance of the catch of the Adriatic tuna and its export to Japan, as it accounts for a large part of Croatian exports.
The two officials also discussed Croatia's upcoming European Union membership, the government said in a press release.
Milanovic said he was sorry about the 2011 earthquake and tsunami in Japan and the many lives lost. "We sympathised with you," he said, adding that Japan continued to donate Croatia even during those tough times.
Prince Akishino and Princess Kiko thanked Croatia for the aid sent to Japan after the disasters.
The royal couple also visited the Dolac produce market and the Zagreb Cathedral. They are on a four-day visit to Croatia.
Later today, Prince Akishino will meet with Parliament Speaker Josip Leko and in the evening with President Ivo Josipovic. Afterwards, the president and the prince will attend a concert on the 20th anniversary of diplomatic relations between Croatia and Japan.