The Rovers boss has defended his decision to block 18-year-old Jones from playing for England Under-19s at the UEFA U19 European Championships in France later this month.
Jones only made his full Premier League debut in March in a 1-1 draw at home to Chelsea but earned rave reviews for his performance.
In May, he signed a five-year deal at Ewood Park and England U19s coach Noel Blake was keen to take him to the tournament in Normandy, which starts this weekend.
But Allardyce has exercised his right to stop Jones going, telling the Lancashire Telegraph: "I don't have a problem with the Football Association.
"We said we would like to keep Phil for our pre-season preparations because we are a small squad and the Premier League starts in a month's time.
"But that was only after we had been told by the FA that he was going to be named in the next U21 squad.
"So we thought, what's the point in him going away with the U19s when he will be in the U21s as soon as the season starts? The FA were fine with that.
"He is a top young player and it's my belief in any case that he will be in the full England squad before very long."