Nunez didn't make the matchday squad for victory over West Ham United last week amid claims the striker had clashed with a member of Slot's staff at training.
But ahead of their match with Leicester City, Slot said: “He didn’t feel himself the day before the match, and he went inside and he wasn’t able to be part of the team the day after.”
The Dutchman was asked directly about the reported row.
He insisted: “No, he didn’t. He did leave the pitch because he didn’t feel himself.”
Meanwhile, Slot also commented on their summer market plans: "I think the core of the team you want to keep as long as you can together, as long as they are performing in the best possible way, but it is also in general good to have some new energy in and around the place with one or two players. That I agree on.
"But it isn’t really a necessity when you look at the quality we have and the quality of the season we have had.”