The former Tottenham Hotspur striker has been without a club since his release earlier this month.
“It is difficult. We admire Adebayor. He is an amazing player but we were, until two weeks ago, having difficulties closing the squad,” said Flores, in quotes published by the Watford Observer.
“At the moment we don’t want to change anything. We respect Adebayor very much and wish him all the best for the future.
“You never know what will happen in football in the future. Maybe we will have the possibility to train together, but at this moment Watford consider it is not the moment to put new players in the squad.”
The Togo international was released by Spurs earlier this month after both parties agree to a termination of his contract.
It followed a summer of speculation and failed deals, with Aston Villa and West Ham United both reportedly close to bringing in the 31-year old - as covered by the Independent.
Flores’ revelation suggests he had concerns over the kind of disruptive effect the former Spurs man could bring to a Hornets side that have enjoyed a solid start to the season.
The Premier League new boys currently sit in 10th place after two wins and three draws from their first six games.
Harmony within a dressing room is vital for a team’s success and allowing Adebayor to join the ranks would have been a risk on the Spaniard’s part.
As it stands, the enigmatic striker is still without a club and will need to look abroad if he is to play any competitive football before the January transfer window.