Stuart Pearce saw his Young Lions tumble out of this summer's European Championship on Saturday after suffering back-to-back defeats against Italy and Norway.
He has had his hands tied by limitations on his squad selection, with the opportunity to call on experienced performers who are now part of national coach Roy Hodgson's plans denied him.
Bernstein understands Pearce's frustration, but insists the FA do all they can to make the playing field as level as possible.
He told Sky Sports News HD: "We believe we do everything we can and we put every effort in to helping all of our managers with their squads, trying to get the best possible squads out for various competitions.
"We have a lot of competitions at the moment with the U21s and the U20s. And of course at the same time, which probably complicated matters, we had two important England friendlies - in particular the Brazil match.
"Although it was only a friendly game, it was a very important preparatory match for the World Cup. Roy Hodgson took it extremely seriously, we all did, and I know he came away having learned a lot about Rio de Janeiro, the climate, the Marcana Stadium, and the whole Brazil thing, which is very special.
"Remember England hadn't played there for 30 years and I think some of the younger players who could have been here that he had there - and (Alex) Oxlade-Chamberlain is a very good example. He only played 30 minutes of football but he came on and helped to change a match that was maybe going the wrong way and put us in a situation where we nearly won for the first time in many years in Brazil.
"I can understand with the World Cup being our main priority - nothing is more important, it can't be in football terms, than the World Cup - that Roy wanted the best squad he could get."
On England's U21 struggles in Israel, which have seen them bow out at the group stage after qualifying so convincingly, Bernstein added: "I was really expecting us to qualify from the group and to get to the semi-finals and maybe the final.
"So to be in the situation where the last match is meaningless is really very disappointing."