"We had a team with 11 changes and there wasn't a lot of cohesion".
Japan were in front at half time, with Ryoto Nakamura and Michael Leitch inspiring the visitors in the first period.
England fly-half George Ford said they did not start their autumn global against Japan with the right attitude.
"The players subconsciously think it's going to be easy and that showed in our attitude and effort, which was disappointing".
"We wanted a game that would test us and we put out a different team and different combinations to see how players were combining in different positions", Jones said afterwards.
"Japan are a hard side to play against if you haven't played them before but I think our second-half response was excellent". "Our attitude wasn't there, which is not good when you're playing for England".
Asked if he had given his side the kind of stern "hairdryer" half-team talk beloved of former Manchester United football manager Alex Ferguson at the interval, Jones joking replied: "It's different these days".
"We just talked about the fact we needed more effort and needed to get stuck in".
Jones was full of praise for Japan, the team he coached to their famous World Cup win over South Africa in 2015 and who host the tournament next year.
"It's fantastic for them".
Current Japan coach Jamie Joseph was also happy with the display, though disappointed at the way the team faded.
"There was a lot of belief in our camp, although 80,000-odd people at Twickenham didn't believe it", he said.
"When it comes down to the crunch we were sloppy in the second half and conceded a couple of soft tries".
"It's a great lesson for us, you want these games to be a lesson".