The division has also changed the rules about when agents are allowed to drink before duty and on presidential trips.
Secret Service spokesman Edwin Donovan said the division's special agent in charge, Dan Donahue, was reassigned to another division.
The Washington Post first reported the changes Tuesday night.
The Secret Service says that in addition to transferring agents from special operations division, anyone assigned to the unit is barred from drinking within 12 hours of starting a shift. They also are not allowed to drink within 24 hours of a president's arrival on a trip.
For now the new alcohol rules about drinking pertain only to the special operations division.
Three agents were sent home from the Netherlands last month after one was found intoxicated in a hotel before President Barack Obama arrived to meet with foreign officials.
It was the latest embarrassing incident for the Secret Service, which faced scrutiny from the White House and Congress after a prostitution scandal in South American two years ago.
Two agents were involved in a vehicle crash in South Florida earlier this year during a presidential trip. The agents involved were not charged with a crime, although it was suspected alcohol was involved.
Secret Service Director Julia Pierson has called the incident "isolated."
"Director Pierson maintains a zero tolerance policy regarding incidents of misconduct," Donovan said.