The Hornets captain has scored eight goals in his debut Premier League campaign and his manager sees him as an option for Roy Hodgson to cover the England skipper's absence
The Three Lions captain could miss up to two months of action after suffering a knee ligament injury, meaning he is likely to miss friendlies against Germany and Netherlands in March.
And Flores believes Hornets skipper Deeney - who has scored eight goals in his debut Premier League season - has the capabilities to step in for Roy Hodgson's side.
"He has the characteristics to play at the high level of the national team," he told reporters.
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"Rooney's injury can be an amazing opportunity for our player and Troy Deeney has the English spirit.
"It would be perfect for the player, it would be perfect for Watford, it will be perfect for everyone."