The $159,096-a-year chief operating officer in charge of O’Hare Airport has resigned, exacerbating a leadership vacuum under Aviation Commissioner Ginger Evans.

Jonathan Leach was a holdover from the team assembled by former Aviation Commissioner Rosemarie Andolino. He served as general counsel before moving up the ladder.

When authority over the massive O’Hare Modernization Project was consolidated under Andolino, Leach assumed more power. As first managing deputy and chief operating officer, he oversaw both day-to-day operations and massive construction projects at O’Hare.

Leach could not be reached for comment. He frequently testifies before the City Council’s Aviation Committee on concessions, leases, construction and most other issues at O’Hare.

Johnathan Leach | Photo from Chicago Department of Aviation website

“Big loss. Without a doubt, almost all major stuff crossed his desk. A lot of institutional knowledge there. He had a lot on his plate,” said a source familiar with Leach’s responsibilities.

The Chicago Sun-Times reported on May 1 that four of Chicago’s top airport security jobs were vacant, a void that raised even more questions about the state of airport security placed under the microscope after Dr. David Dao was dragged off a United Airlines flight by aviation security officers on April 9.

The high-level vacancies included fired O’Hare and Midway security chief Jeff Redding; two deputies who’d been working under him, and the managing deputy commissioner of security who was supposed to be Redding’s boss, City Hall sources said then.

At the time, Evans told associates the vacancies were hampering her ability to investigate the passenger-dragging fiasco. She also complained that, in some cases, the salaries for the jobs are too low to lure top talent away from other major airports.

Andrew Velasquez, the former regional administrator for the U.S. Department of Homeland Security, has since replaced Redding, who was fired from his $118,020-a-year job for failing to fully disclose the sexual harassment allegations that prompted the Illinois Tollway to get rid of him.

As managing deputy for safety and security, Velasquez will be paid an annual salary of $175,000. That’s more than $56,000 higher than Redding’s salary as deputy commissioner.

Sources said the chief of staff’s position remains vacant, as well as the job of chief counsel. Another deputy for security was reportedly hired earlier this week.

Aviation Department spokeswoman Lauren Huffman had no immediate comment on Leach’s departure.

Another source said Evans “hopes to announce a new, highly qualified” chief operating officer shortly.

Along with Velasquez, Leach’s replacement is likely to play a pivotal role in determining whether the city’s force of aviation police officers should continue to exist in the wake of the United fiasco.

That question has yet to be resolved and will be complicated by opposition from the Service Employees Union Local 73, which represents the 292 officers.

Contributing: Tim Novak