Just as members of the England squad arrived at a youth development project in Rio de Janeiro, Ferdinand rekindled the argument of English football being in the "Dark Ages" by claiming that changes need to be made to help the next generation of players become stars.
Bernstein told Press Association Sport: "Rio Ferdinand should know that we are putting a huge amount of work in to that (youth development)."
He added: "We are implementing a complete programme of youth development football within the leagues, with the EPPP (Elite Player Performance Plan) system and with the opening of St George's Park. All those things are in hand.
"They are not producing the results yet but they will do. These things take a while as we know but these things are in place there is a huge amount of work taking place and I think potentially we are in a very decent shape.
"I am sure when he reflects on it Rio and others will appreciate that this is happening, it's not talk about what might happen. It is happening, a lot of work is going in to it and a lot of people are working very hard."
The discussion about the state of the English game has been rumbling on since former England striker Gary Lineker published a downbeat tweet on the matter following Wednesday's 1-1 draw against the Republic of Ireland at Wembley.
Manchester United defender Ferdinand, who quit international football earlier this month, was one of the so-called 'golden generation' of English footballers who blossomed at the start of the last decade but failed to deliver on the big stage.
Ferdinand said on Twitter: "[In the] last 10 years when have England played consistently well? A coaching strategy for our young teams/kids needs to be implemented to see change. In most PL teams retaining the ball is done best by foreign players in the team.... they are taught to pass to a man with a man on.
"[The] So-called 'Golden Generation' obviously wasn't because we won nothing! Great players don't always make great teams.''