The Spain international has been heavily linked to the Red Devils for some time, but conflicting reports have caused confusion over the status of the proposed transfer.
It has been claimed that the 24-year-old cut short his honeymoon with new wife Alice Campello in order to push through the move to Old Trafford.
However, Perez has suggested that Los Blancos are not yet involved in any deal and have certainly not reached an agreement with the Premier League giants.
"I think we're not in negotiations with Manchester United, which is not to say that there are people around you who are talking, which is normal," Perez told esRadio. "I have read that we have reached an agreement I do not know how many million times, but it isn't true."
Morata scored 20 goals in 40 appearances in all competitions last season.