Two top Thruway Authority officials resigned on Wednesday as the authority faces questions over tolls, its operations and how it will pay for the new Tappan Zee Bridge.

Executive Director Thomas Madison and Chief Financial Officer John Bryan turned in their resignations, according to an email sent Wednesday from Thruway Authority Board of Directors Vice Chair Donna Luh to employees. The resignations came as the state Inspector General’s Office is reportedly finishing up an investigation into the authority.

They also follow the resignation of Thruway Authority Chair Howard Millstein in early December.

“Both are outstanding public servants who have led our organization through some very challenging and exciting times,” Luh wrote of Madison and Bryan. “The Board and I wish them all the best as they leave to pursue new opportunities, and thank them for their many years of dedicated service. Leadership changes at the Authority are part of a natural transition of government, and I am working closely with fellow Board members and Authority staff to assure a smooth and efficient transition process.”

Madison said in a statement that it has been an honor to serve in the Cuomo administration.

“It was a particular privilege to be a part of the leadership team of the New NY Bridge project to replace the Tappan Zee and to serve alongside so many talented and committed public servants,” he said.

Deputy Secretary of Transportation Karen Rae will manage the transition, while Jennifer McCormick, assistant deputy director of state operations, will take over day-to-day operations until a new executive director steps in.

Gov. Andrew Cuomo nominated Madison for his post in 2011. Before that, Madison worked for the state and federal transportation departments. The Daily News reported last week that the Cuomo administration had approached possible replacements for Madison amid the inspector general’s investigation.

Bryan had served as chief financial officer since 2004.

According to data from SeeThroughNY, a website sponsored by the Empire Center for Public Policy, both men made more than $175,000 in 2013.

The resignations come at a tumultuous time for the Thruway Authority, as it faces scrutiny from the construction of a $3.9 billion replacement for the Tappan Zee Bridge.

The authority recently released a $2 billion spending plan, which did not include projected toll increases. But fears have been raised that tolls along the 570-mile highway system will have to increase to help finance the project.

The Thruway Authority has taken public relations hits elsewhere as well, most recently in November, when seven feet of snow buried the Buffalo region. Some Thruway motorists were stranded by huge snowdrifts for more than a day.

Madison and Bryan join other top state officials who stepped down before the first of the year. Capital New York reported Wednesday that Department of Motor Vehicles CommissionerBarbara Fiala submitted her retirement papers. Office of Temporary and Disability AssistanceCommissioner Kristin Proud and Labor Commissioner Peter Rivera also have left their jobs.

© 2015 Albany Times Union