It was previously reported that the England striker's relationship with manager Sir Alex Ferguson had broken down, with the Scot prepared to offload him for £40m.
However, Gill has now clearly stated that Rooney is not for sale at any price, reports The Sun.
"Wayne is definitely not for sale and I can categorically say there has been no discussion within the club or with his agent," he is quoted as saying.
"He is in a long-term contract with us and is very integral to our team."
Speculation over the player's future began to mount after he was excluded from the starting XI in last weekend's Premier League clash against Fulham.
Rooney featured as a substitute in the game, but suffered a severe gash to his leg, leaving him sidelined for up to two months.
"Wayne's a great player who has got a bad injury - but he will come back," Gill added.
"He didn't start on Saturday for various reasons. Alex Ferguson picks the best team to win the game and that's it.
"He's a manager who's been so successful and there will be rotation."
Rooney has made 253 Premier League appearances for United since joining from Everton eight years ago, scoring 129 goals.