WASHINGTON — John S. Pistole, the administrator of the Transportation Security Administration, whose decision to put in place more aggressive pat-downs and full body scans at airports drew wide criticism, is stepping down, the agency said Thursday.

Mr. Pistole, a former deputy director of the F.B.I., was nominated to the post by President Obama in 2010 after the president’s top two choices were forced to withdraw because of questions raised about their past.

Mr. Pistole took over the agency at a delicate moment, after the near escape of Faisal Shahzad, the suspect in a bombing attempt in Times Square, who managed to buy a plane ticket to Dubai even after his name had been flagged by the F.B.I.

He moved quickly to expand security measures at airports to include full body scans and pat-downs, becoming the face of many Americans’ frustrations with airport security, even drawing a nationwide protest.