Striker Michael Owen poached his 25th goal for England in the 22nd minute, but midfielder Shinji Ono deservedly levelled for Japan on 53 minutes.
England coach Sven Goran Eriksson will want his side to move up a gear in time for the Euro tournament in Portugal.
Japan looked by far the sharper and more fluid side at the City Of Manchester stadium on Tuesday night.
The match also resulted in some injury concerns for Sven.
David Beckham received treatment for an ankle problem and John Terry went off near the end with a hamstring injury.
Then, in the dying minutes of the game, Gary Neville took a heavy knock and limped off, to be replaced by his brother Phil.