Leclerc came home 0.589sec behind triple world champion Max Verstappen, who made it four pole positions from four grands prix so far this season.
Leclerc also trailed teammate Carlos Sainz, who qualified in fourth, with the Monegasque driver saying it was “definitely not a good feeling”.
“I tried many different things today and none of them worked,” Leclerc told Sky Sports.
“For now, I don’t have the answers but the positive thing, if we have to find one, is our race pace looks a bit stronger.
“But on a track like this, qualifying position is extremely important and today we didn’t do a good job.”
Sainz led Leclerc to a one-two finish for Ferrari at the Australian Grand Prix a fortnight ago, with Verstappen retiring from the race with a brake issue.
But while Sainz said he was happy with his qualifying performance in Suzuka, Leclerc cut a frustrated figure.
“I’m not happy with our qualifying today,” he said.
“The feeling in the car was quite good but the pace was just not there, so we will look at the data and assess what exactly this was down to.”
Verstappen qualified 0.066sec ahead of Red Bull teammate Sergio Perez, with McLaren’s Lando Norris coming home in third.
Sainz said he thought his fourth-place finish left him “in a good position to fight tomorrow”.
“We’ve made good steps in terms of race pace and I hope we will be able to exploit it during the race and fight for a podium position,” said the Spaniard.
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