Moody was on Monday ruled out of England's opening showdown with Argentina after failing to recover from a knee ligament strain in time.
The Bath flanker had been due to make a full return to training for the first time since suffering the injury in England's victory over Wales on August 6.
But the England medics declared Moody, who has been running and doing some training, was not right for a full contact session and Johnson decided not to risk him so early in the tournament.
It was something of a gamble for Johnson to travel with an injured captain in the first place - but he insisted replacing Moody in his 30-man squad was not on the cards.
Moody's next target it to prove his fitness to face Georgia in England's second World Cup fixture, a week on Sunday.
"It is the opening game of what hopefully is a long tournament so you can force these things sometimes and that can go either way," said Johnson.
"He has been running around today so he is not a million miles away. We hope he should be fit (to play Georgia).
"We thought he would be fit for this one. The medics had hoped he'd be ready
to go but he's not quite there. We are in a World Cup and it adds to the emotion of the whole thing.
"At their clubs they might be given until later in the week often, but we want to have a good full week of training this week with everyone ready to go.''
Mike Tindall captained England in Moody's absence through the RBS 6 Nations and in their last two warm-up games, against Wales away and Ireland at the Aviva Stadium.
James Haskell enjoyed an impressive Six Nations at openside and he is the obvious choice to start in the number seven jersey against Argentina.
Johnson will confirm his line-up to face Argentina on Thursday and Haskell's recent form for England clearly eased the disappointment of losing Moody.
"We are very happy with the other guys so it is a very simple decision to hold him back another week,'' said Johnson.
When Moody was named in the squad, Johnson admitted that not every player would have been allowed to carry an injury into the tournament.
But Moody's captaincy has been intrinsic to England's upturn in fortunes over the last 18 months and wing Chris Ashton confirmed he will have a vital role to play this week despite his injury setback.
"It is always a blow to lose your captain and he is a man of such experience, having played in three World Cups,'' said Ashton.
"But he is still around the squad. We are all together and a tight group and together all the time.
"He is not going to be on the field but he is going to with us right up until the end.
"It is disappointing but there are other people who can step up in his place. James Haskell played really well last week against Ireland and there are other lads who can step into that position."
Moody first injured his right knee in January playing for Bath, which ruled him out of England's Six Nations title-winning campaign.
The veteran flanker suffered the recurrence when Tom Palmer fell on him at a lineout, 62 minutes into the warm-up win over Wales at Twickenham.
Moody immediately feared for his World Cup place but the heavy strapping he was wearing saved him from more serious damage - and as recently as Thursday he felt "on the right path".
England's other walking wounded have all returned to full training, with scrum-half Ben Youngs in contention for selection after overcoming his summer knee operation.
Tom Wood and Nick Easter both missed the Ireland game as a precaution with calf problems but they played a full part in training, as did Mark Cueto who struggled in Dublin with a lower back problem.
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