Julen Lopetegui was dismissed before the World Cup after taking the Real Madrid job, and Fernando Hierro was brought in on a temporary basis. However, La Roja were eliminated at the last-16 stage after losing on penalties to Russia.
Hierro is not expected to continue in the position on a full-time basis and according to AS, Flores is in contention to become the long-term replacement for Lopetegui.
The 53-year-old is available after leaving Espanyol in April, while the former Spain international has also managed the likes of Valencia, Atletico Madrid and Watford.
Roberto Martinez is another to be linked with the role after winning 18 of his 24 matches in charge of Belgium, who have reached the quarter-finals of the World Cup.