Jets executive chairman Shane Mattiske said Harper was entitled to his opinion and welcomed his passion for the club.
"There's no question that there was a disruption before the season started with the change of ownership," Mattiske said.
"We've had to re-launch the club and start from scratch.
"The reality is that the squad we have now is the one that we were left with. We've been working hard on improving the resources, finishing this season competitively and building a much stronger squad for next season."
Mattiske saw no value in debating Harper's claims point by point.
But in fairness to the Jets, at the end of last season they lost former Socceroos Dimi Petratos and Bernie Ibini, ex-Premier League stars Wes Hoolahan and Joe Ledley, veteran goalkeeper Glen Moss, Nick Fitzgerald, a veteran of 189 A-League games, and Panamanian international Abdiel Arroyo.
Injuries have also sidelined senior players Nigel Boogaard, Ben Kantarovski, Jason Hoffman and Johnny Koutroumbia for long stretches this season.