Pearce recently launched a verbal attack on England's youngsters by questioning their desire to represent their country at a lower level.
"The FA are disappointed with the comments of Stuart Pearce with regard to squad selection this summer," read an official FA statement.
"Squads were selected for the summer tournaments and decided upon by the coaching staff, including Stuart Pearce. The players were then advised accordingly which squads they were in.
"It is unfair to criticise individual players. All selections were management decisions and were not taken by individual players."
Pearce took charge of the Under-21s in 2007 before being dismissed from the role earlier this year following the team's poor performance in the European Championship.