Ferguson left Rooney out of the United line-up for Tuesday's Champions League defeat by Real Madrid, since when it has been suggested the Red Devils boss would be willing to accept an offer for the striker this summer.
However, speaking ahead of Sunday's FA Cup quarter-final with Chelsea, Ferguson denied that was the case.
"He will be here next year, you have my word on that," he said.
"There is no issue between myself and Wayne Rooney. To suggest we don't talk is nonsense.
"He understood the reasons completely. Tactically we got it right. We don't always but we did then.
"There are no issues with the player and he will be involved on Sunday.
"I left out Shinji Kagawa after he scored a hat-trick. I thought I would get more stick for that."
Ferguson is still bitter about the circumstances of Tuesday's defeat, in particular the dismissal of Nani, on which the entire contest turned.
"It is hard to keep your faith when you have things like that," said Ferguson.
Ferguson refused to say whether Rooney would actually start on Sunday.
And he again repeated his belief that the 27-year-old needed to play matches in order to retain full fitness, an assessment that has raised so much debate over the past few days.
"Why should I help anyone by telling them my team? We don't do that," said Ferguson.
"But Wayne does need a lot of football. He has always been that type. That has always been the case."
Ferguson said he had been concerned about the appointment of Turkish referee Cuneyt Cakir prior to Tuesday's game.
Cakir has now sent off seven players from English teams, but never one against them.
"I was concerned. I said that to my staff," he said.
"I had a big worry about it but it is gone now. There is nothing we can do about it."
Meanwhile, Ferguson confirmed Phil Jones was still not fit enough to return after an ankle injury, although could be available to face Reading in the Premier League next Saturday.
And the United boss admitted Nani may need a lift after his unfortunate experience in midweek.
"Nani was obviously disappointed and we have to get rid of that feeling of guilt he maybe has," said Ferguson.
"I don't think he did anything wrong and that's the message we'll give to him."
Ferguson also opted against attacking old adversary and the under-fire Rafael Benitez, whom he faces at Old Trafford for the first time since his surprise arrival at Chelsea.
"I'm not going to kick anyone when they're lying down," he said.
"It's not my style."
However, a meeting with Chelsea offers the perfect pick-me-up after the Champions League exit.
"In the cold light of day, though, we're Manchester United and we have to get on with it," said Ferguson.
"There's nothing that can be done now. We have an important issue of a quarter-final on Sunday.
"I've cleared my mind. It's just another day in the history of our club. Not a good day, but another day."