"Given it is a Champions League match, it is considered high risk and security will be reinforced," the local government said in a statement.
Unlike league matches between the two where away allocations are restricted to a few hundred tickets, UEFA rules mean Atletico will have a large travelling support of around 4,000 at the 80,000 capacity Santiago Bernabeu.
The number of security personnel will be even higher than Madrid's last European home game against Bayern Munich when riot police clashed with visiting fans at half-time.
There were also violent clashes before Atletico's quarter-final home tie between police and Leicester City fans, eight of whom were handed suspended four-month jail sentences.
UEFA has also vowed to reinforce security around Champions League games following a triple bomb attack on the Borussia Dortmund team bus ahead of their quarter-final, first leg with Monaco.