Captain Lewis Moody will not play in England's opening Rugby World Cup match against Argentina on Saturday after failing to recover from a knee injury.
The 33-year-old suffered a recurrence of the ligament injury in England's first World Cup warm-up game against Wales at Twickenham on 6 August.
Moody hurt the knee playing for Bath in January and missed the Six Nations.
"We hoped he would be fit to start training but he is not quite there", Johnson said.
Moody said on Thursday he was hopeful of adding to his 67 caps and was "on the right path" to proving his fitness for the clash against the Pumas.
But the skipper, who has played only 62 minutes of Test rugby this year, will not be risked with England's next fixture on Sunday, 18 September against Georgia.
Johnson said he was confident Moody would still play a significant role in the tournament.
"He has been running around today so he is not a million miles away," Johnson added.
"It is just one of those calls, 'are you ready to participate fully this week and play a Test match this Saturday?' Not quite."
Meanwhile, defence coach Mike Ford says England face a stern test in the group stage of the Rugby World Cup but that it could serve them well for later in the event.
"You don't want to go to a quarter-final winning by 100 points in every game," Ford said of Group B, which pairs England with Argentina, Scotland, Georgia and Romania.
"If you are not on your game in this tournament you will probably lose.
"We are probably in the group of death as Scotland are playing very well.
"If we don't treat Argentina with the utmost respect we will come unstuck."
Johnson's side won their final warm-up game 20-9 against Ireland, a match that Ford saw as perfect preparation for the challenges ahead during a tournament that finishes on 23 October.
England's bid to match their 2003 World Cup triumph has been backed by All Blacks assistant coach Wayne Smith.
The former Northampton Saints coach has been impressed with the way Johnson has improved the fortunes of the team since he took over in April 2008.
"They were brilliant. Martin Johnson has done a really good job. He's given them a lot of belief. They come out here with a squad that has developed its game hugely from basically a 10-man rugby team to playing 15-man rugby.
"I think that makes them a real danger."