As a result, Wasps' uncapped 23-year-old Joe Simpson received an unexpected call-up to join Leicester's Ben Youngs, who is on the way back from knee surgery, and Saracens' Richard Wigglesworth.
Johnson telephoned Flutey reluctantly to tell him the bad news - and even on Monday the England manager mounted a strong argument for why the 2009 Test Lion should have been selected.
Not only would Flutey have offered a creative, kicking option at inside centre, but he could provide cover at both fly-half and scrum-half in case of emergency.
Instead, England opted for three specialist scrum-halves in a squad comprised of 17 forwards and 13 backs, shifting the focus of their gamble into the midfield.
Wigglesworth will have to provide emergency fly-half cover should any mishap befall Jonny Wilkinson or Toby Flood.
Shontayne Hape, the former Kiwi rugby league international, travels back to New Zealand as the only recognised inside centre in England's 30-man squad.
"Would I love to have Riki on the plane? Of course I would,'' admitted Johnson.
"It was tough on Riki, who has done nothing wrong. We just felt that was the best way to go.
"Someone like Riki would have been ideal (to cover at 10). He can play a bit of nine too but you have to make a call somewhere.
"Utility is good but it is not the trump card. We just felt we had to go with five props and four locks because of the attrition rate and it was too big a risk to take two scrum-halves.
"Any solution leaves you slightly thin somewhere. If we get an injury in the front row I will look like a genius. If we get one at inside centre ...
"We can probably cover at 10 a little bit easier than nine. It is a very specialist position. Yes, it won't be great if we have two injuries at 10. But like hooker, nine is a specialist position. You need a guy there who can do it.
"Ben Foden has played a decent amount of rugby there but not for a while. Riki could cover nine as well but we thought it was a risk we couldn't take."
Flutey was a Test Lion in 2009 but injuries and an unsuccessful spell with Brive stalled his career and Hape has since cemented his place as England's inside centre.
Leicester powerhouse Manu Tuilagi, who made a try-scoring debut against Wales at Twickenham, made the final cut along with Mike Tindall and Matt Banahan, suggesting England's midfield approach will not be subtle.
Toby Flood and Jonny Wilkinson are the only fly-halves in the squad, Mark Cueto and Chris Ashton the only recognised wings.
Johnson said he would consider using Flood and Wilkinson together, although if that was a serious option England would surely have selected Charlie Hodgson as a third fly-half.
"We cover all these things when you are putting the squad together. We know Toby can play 12,'' said Johnson.
"We often finish with them at 10-12 so we know the options that are there. We have a great option with Jonny if we need to and want to."
Banahan and Simpson are both able to fill in out wide while full-backs Foden and Delon Armitage complete a 13-strong backs contingent.
Up front, England have opted for five props - Dan Cole, Matt Stevens, Andrew Sheridan, Alex Corbisiero and David Wilson - and four locks.
Dylan Hartley, Steve Thompson and Lee Mears were confirmed as the three travelling hookers after phase one of the England's summer training camp, when George Chuter was cut from the squad.
Johnson had been considering taking only three locks and utilising Tom Croft or Nick Easter as an emergency second row but England have decided to take four.
Veteran Simon Shaw has been picked alongside Courtney Lawes, Louis Deacon and Tom Palmer, leaving only five back-row places available.
Lewis Moody, who is on the way back from a knee injury, captains the squad and is joined in the back row by Easter, Croft, Tom Wood and James Haskell, leaving no room for the specialist open-side flanker Hendre Fourie.
"It wasn't so much the names as the composition of the squad that was tough,'' said Johnson.
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