Flores said the reigning European champions would pull through the group stage after their opening 1-0 loss and live up to their billing of being one of the tournament favourites because they had the best coach and players available.
"Vicente Del Bosque is a motivator, he has my respect as the best coach Spain could have and he will inspire the team to qualify from the group and go further," Flores told Reuters in an interview on Sunday.
"The team did not play well against Switzerland but these are exceptionally good players and I am sure they will improve for their next two group games.
"Fatigue was obvious in the opening game because the Spanish league and the Premier League, where the national team's best players perform, are very strong and it's been a very long season for all of them."
Spaniard Flores, who won the Europa League with Atletico last season, said Argentina had so far stood out in a mediocre World Cup with no clear favourites to win the title.
"I like how Argentina have played so far but I don't see any favourites at this moment and the tournament has produced nothing special so far, there hasn't been too much quality," he said.
Spain play Honduras in Johannesburg at Ellis Park on Monday and meet Chile in their final Group H match in Pretoria on Friday.
