In a low-key, disjointed match which featured another penalty miss by Frank Lampard, Fabio Capello was given little help if he was still unsure which seven players to jettison from his 30-man squad on Tuesday or even which formation to use.
The Italian had a 30-minute second-half flirtation with the impressive Wayne Rooney as a lone striker supported by Joe Cole but soon reverted to England's traditional 4-4-2.
Neither approach produced a goal for a man in a red shirt as Japanese defenders Tulio Tanaka and Yuji Nakazawa both put through their own net in the second half after Tulio had given them a sixth-minute lead.
Japan, whose coach Takeshi Okada offered to resign last week after defeat by South Korea, will be pleased with their tireless efforts and take some comfort from the fact that England's second-half keeper Joe Hart had to make several good saves.
England, who looked lively at times in beating Mexico last Monday at Wembley, were slow out of the blocks and paid an early price as poor marking at a corner allowed Brazilian-born Tulio to turn in a low shot from the edge of the box.
England were given the chance to equalize after 56 minutes when two Japanese defenders handled a Lampard free kick but the Chelsea midfielder, who missed a penalty in the FA Cup final two weeks ago, saw his low effort well saved by Eiji Kawashima.
Japan substitute Takayuki Morimoto had a crisp shot well saved by Hart after 67 minutes and Kawashima more than matched him with a superb diving save to tip clear a Rooney curler.
NO CHANCE
The Japan keeper had no chance with the equalizer though as Tulio turned a Joe Cole cross into his net while attempting to head it out for a corner after 72 minutes.
He was left similarly wrong-footed seven minutes from time as Nakazawa diverted a low Ashley Cole cross into his own net.
Emile Heskey should have added a late third from a lovely Steven Gerrard cross but headed wide.
Capello said after the match that he had already decided which seven players he will cut. He has given midfielder Gareth Barry extra time to recover from an ankle injury but the likes of Michael Dawson, Stephen Warnock and Scott Parker, who have not featured in the last two friendlies, are likely to be making alternative summer plans.
"I know my 23 players, yes," Capello told ITV. "As for today, I'm happy for the second half. In midfield we played better, faster and found space. In the first half we were too slow and it was easy for Japan to defend.
"It was an interesting game for me. I saw a lot of players who didn't play before and learnt more about them."
England finished the game with Gerrard and Lampard playing together in midfield, something that has rarely worked under successive managers but which might crop up again if Barry fails to recover.
"They've never played together in the center under me, but they played well," said the Italian. "They are good players, fast, with good quality and good going forward."
Joe Cole, who has probably done just enough since his return from long-term injury to make the cut, said he had trained as a second forward with Rooney only once. "You have to have options and I enjoyed it," he said. "I've had a good 10 days training and a good 45 minutes I just want to help England win the World Cup."
They begin their bid on June 12 against the United States followed by matches against Algeria and Slovenia.
Japan kick off their daunting Group E campaign against Cameroon on June 14 before taking on Netherlands and Denmark.
