Stones has been linked with a £1.5million move to Fulham.
But boss Flitcroft insists the 18-year-old needs to learn his trade in the Championship before a switch to the Premier League.
Flitcroft said: "I don't think the boy is ready - and he would admit the same. If there was a deal out there it would have to favour the club.
"If he does leave, it is important we keep him on loan for this season because he is developing.
"I think the club is realising that some of the valuations out there are disrespectful."