Tonge, 27, joined Derby on loan in February until the end of the season and has since made 16 appearances and scored two goals.
The midfielder joined the Potters in September 2008 but has struggled to hold down a regular first-team place.
Clough said: "He has got two years left on his contract at Stoke and is on Premier League money and I don't think we can stretch to that at this stage.
"He says he wants to stay, he is enjoying it and he wants to play football. He has started every game for us since he has been here."