WASHINGTON — Facing a backlash over long security lines and management problems, the head of the Transportation Security Administration shook up his leadership team on Monday, replacing the agency’s top security official and adding a new group of administrators at Chicago O’Hare International Airport.

In an email to staff members, Peter V. Neffenger, the T.S.A. administrator, announced a series of changes that included the removal of Kelly Hoggan, who had been the assistant administrator for the Office of Security Operations since 2013.

Beginning late that year, Mr. Hoggan received $90,000 in bonuses over a 13-month period, even though a leaked report from the Department of Homeland Security showed that auditors were able to get fake weapons and explosives past security screeners 95 percent of the time in 70 covert tests.

In addition, several employees who say they were punished with reassignments to other airports after filing whistle-blower complaints have alleged that Mr. Hoggan played a role in their forced transfers.