The Portuguese club have been looking for a new coach since José Antonio Camacho resigned from the post on March 9th, following a series of bad results.
Fernando Chalana, who was appointed interim boss, is coming under increasing pressure after a 3-0 home defeat to Académica de Coimbra, which left the club in fourth place with only four games left.
Flores has been without a job since he was sacked by Valencia in late 2007, but turned down the offer to coach the Eagles as he was not interested in a short coaching experience.
"Benfica, Olympiacos and Besiktas wanted an immediate arrival, but I am not a temporary coach, a six-month coach," he told El Mundo Deportivo.
Meanwhile, Manuel García Quilón, Flores' representative, added: "I was contacted by an agent, asking if Quique Flores could immediately start working until the end of the season.
"We said no, because a situation like this does not interest us. Quique Flores wants another type of project, starting from the beginning of the next season."
Flores initiated his coaching career at Real Madrid's youth team, and after two years in charge of Getafe, he was appointed coach of Valencia, having guided Los Che to the Champions League quarterfinals.
Goal.com - Portugal - Flores Says No To Benfica