Johnson confirmed he was involved in the decision to ban Jonny Wilkinson's kicking mentor Dave Alred and fitness specialist Paul Stridgeon from Saturday's decisive Pool B showdown with Scotland.
The two coaches had illegally switched the ball Wilkinson was due to kick conversions with on a number of occasions during the first half of England's 67-3 victory over Romania.
The Rugby Football Union were forced to act after England became the subject of a misconduct investigation by Rugby World Cup Limited (RWCL).
Johnson and Wilkinson avoided having to answer any official questions from RWCL on their own involvement, or lack of, after the tournament organisers accepted England's action and chose not to launch a further investigation.
Alred and Stridgeon helped put the England squad through their final paces at Eden Park on Friday - but both will be banned from entering the stadium on Saturday.
"I am responsible for everything that happens here,'' Johnson said.
"Of course the RFU are involved as well but it was also my say (to implement the bans). I'm part of the RFU, I'm an employee of the RFU.
"Paul and David did what they did in the heat and confusion of a Test match.
"I don't suspend guys lightly. We regret what we did and it was wrong.
"In the heat of a World Cup match these guys have made a mistake and they had paid for it.
"We should have asked the referee (if they could switch balls), we didn't.
They asked us to stop, we did.
"Paul is gutted by this, getting something wrong. He is upset by it, as is
This latest brush with authority comes after an eventful World Cup campaign for England, who were reprimanded by tournament officials after their shirt numbers peeled off in the opening game against Argentina.
Johnson then had to face down criticism over his players' conduct on a drunken night out in a Queenstown bar that was hosting a dwarf-racing competition.
Mike Tindall also found himself at the centre of a media storm after being
captured on CCTV at the Altitude Bar in conversation with a woman.
Johnson, who was captain at the 2003 World Cup when England became embroiled in the 16th man incident against Samoa, is confident 'ballgate' will not distract his men from the task at hand.
Eight years ago, England were fined £10,000 after briefly fielding an extra player against Samoa and had fitness coach Dave Reddin banned for two matches for a verbal altercation with fourth official Steve Walsh.
"The 16th man thing had to be dealt with, the management dealt with it and the players got on with playing,'' Johnson said.
"It's the same in this instance.
"If you are derailed by things like this you're not going to give yourself any
chance. It's a bump in the road, we got it wrong, we've put our hands up and we'll move on.
"When you come to a World Cup you don't expect it to be a smooth ride. These things happen in tournaments and you just get on with it.''
And getting on with it will mean England beating Scotland in Auckland on Saturday, topping Pool B and booking a quarter-final with France.
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