The Bulgarian international's agent said on Friday that the Premier League champions had sounded out Tottenham about a potential move.
But chief executive David Gill issued a denial, saying: "We have categorically not made a bid for Dimitar Berbatov."
Spurs added: "We have not received an offer and would not accept one if we did - it is as simple as that."
Speaking on Bulgarian radio, his agent Emil Dantchev said: "We had a 90-minute meeting with Tottenham's chairman Daniel Levy and sporting director Damien Comolli.
"They informed us that there's a query from Manchester United about the possibility of Berbatov joining them.
"They told us they will have a meeting in the next day or two to decide his future."