Japan scored four goals in three group games
Japan stunned Spain and Germany to win Group E and reach the knockout stage for a fourth time.
Croatia, runners-up in 2018, stand in the way of Japan's first World Cup quarter-final.
Nagatomo said that "the first condition is to have courage" at the Al Janoub Stadium in Qatar.
"Before they go into battle they (Samurai) polish their weapons and try to improve their techniques," he said.
"But if they are scared during battle, they would not be able to use those weapons and techniques fully.
"It's exactly the same with football. Of course the tactics and techniques are important, but no matter how much we have improved those, if we are scared when we are on the field, those things are useless."
Croatia failed to score against Morocco and Belgium, but a 4-1 over Canada ensured they progressed as Group F runners-up.
Manager Zlatko Dalic said of Japan's stunning 2-1 win over Spain: "When Spain scored the opening goal, I thought Japan were finished, but they never gave up and deserved their victory.
"The fact that Germany, Belgium and Denmark have all been eliminated illustrates just how strong other teams have been at this World Cup.
"In the past, I might have picked Japan as an opponent that we would want to play, but they have defeated both Germany and Spain. This certainly will not be an easy game for us."
Japan defender Ko Itakura is suspended so Takehiro Tomiyasu is in line to replace him as he is now fit enough to start, having been hampered by a hamstring injury at the start of the tournament.
However, Takefusa Kubo missed training on Saturday due to muscular discomfort, while Hiroki Sakai is still troubled by the thigh problem he picked up in their match against Germany.
Croatia boss Zlatko Dalic made just one change during his side's three group stage games and could again stick with the same team that played against Canada and Belgium.
-- Courtesy of BBC Sport