Sanchez Flores guided Atletico to victory in the Europa League final and runners-up spot in the King's Cup last season but has been questioned after a disappointing run of form.
Atletico are out of the Europa League, were dumped out of the King's Cup by city rivals Real and lost 1-0 at struggling Sporting Gijon on Sunday to slip 10 points off the Champions League qualification slots.
"Sanchez Flores will be coach until the end of the season. At the end of the campaign we will talk," majority shareholder Miguel Angel Gil told the club website.
Real Madrid's search for a striker to stand in for the injured Gonzalo Higuain has seen Atletico's Argentina international Aguero linked with a move to the Bernabeu, but Gil said they had rejected the approach.
"In the last week we have received two offers," Gil added after a visit to the club's training ground.
"One from Real for Aguero for 45 million euros and the other from Chelsea for Aguero and (Uruguay defender) Diego Godin for 60 million.
"Atletico have said no to the two offers because they believe in these two players."
After selling Simao Sabrosa and buying in Elias and Juanfran, Gil said there would be no more activity in the January transfer window.
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