The Japanese pulled off an incredible 34-32 victory over South Africa in their opening game but four days later they looked jaded and disorganised against the Scots.
"We weren’t good enough under the circumstances," Jones told reporters on Thursday.
"In retrospect, I got a number of things wrong. I got selection wrong, I didn’t have the players mentally right for the game. They are all my responsibilities. I take full responsibility for the defeat and performance."
Jones said the team needed to refocus for the game against Samoa on Oct. 3.
"Everyone’s disappointed about the result but part of the World Cup is having the ability is to move on to the next game," he said.
"At the start of the tournament, if we knew if we had one win and a loss after two games we’d be pretty happy.
"We’re disappointed because we felt like we could have won two games. But the reality is we’re in a perfect situation to achieve what we came here to achieve, and that’s to make the quarter-finals."
Japan have been under an intense media spotlight since the win over South Africa, the biggest upset in Rugby World Cup history.
"Mentally, we have to get it right," Jones said.
"The team has experienced an entirely different environment at the World Cup. Not in the wildest dreams did we expect to get the attention we’ve been getting.
"Maybe the players have lost a little focus, so it’s my job to get the focus back. We had some players who just didn’t back up very well from the previous game. And that’s my mistake, so I have to get the selection right for the next game."
Fullback Ayumu Goromaru was criticised for missing a few kicks against Scotland.
"I’m not a machine so I’m going to miss every now and then," he said. "I’m not bothered by it at all.
"We’ve trained harder than any team in the world. Our strengths came to the fore against South Africa and our weaknesses surfaced against Scotland. For us to become a tier one nation, we need to be more consistent."
(Reporting by Ed Osmond; editing by Justin Palmer)
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