The FA sacked Pearce in June following the representative side's terrible campaign at the European U21 Championships in Israel.
England lost all three of their group games and scored just one goal to be eliminated from the tournament but, this week, Pearce has blamed the likes of Manchester United's Jones and Danny Welbeck, plus Arsenal pair Alex Oxlade-Chamberlain and Jack Wilshere for their commitment to the junior team.
Pearce said Oxlade-Chamberlain and Jones were not included in England's squad because 'they didn't want to come' but the FA has hit back at the 51-year-old former coach.
"The FA are disappointed with the comments of Stuart Pearce with regard to squad selection this summer," a statement from the FA said.
"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."
Jones has reportedly been particularly incensed by Pearce's comments, which stemmed from the comparison between England's squad - which was shorn of its best players who regularly play for the senior team - and Spain, who won the tournament with the likes of David de Gea, Iker Muniain, Isco and Thiago Alcantara involved.
"Once they go through the golden ivory towers of the seniors they don't want to come and play with the Under 21s anymore," Pearce said.
"There is no nation in the world that could suffer that.
"Our boys, for whatever reason, be it the power of the Premier League, the finance they get at such a young age, whatever it may be, there is a lack of real passion to want to play for your country no matter what.
"We have to solve that problem and give them international experience."
