The new secretary vowed to act “aggressively” in holding people accountable, but since taking control he has fired fewer employees than his predecessor did in the year before he resigned. Mr. McDonald was forced to backtrack in February after claiming on “Meet the Press” that 60 employees had been fired for manipulating wait times. A spokesman later said it was fewer than 20.

The director of the Phoenix hospital, Sharon Helman, was fired in December for accepting improper gifts, not for her role in the scandal. Lance Robinson, the associate director, and Brad Curry, the health administration services director, have been on paid leave for nearly a year, and have been issued “notices of proposed removal,” according to a department spokesman. Another spokeswoman said the investigation of them was continuing.

Dr. Darren Deering, the hospital chief of staff, who told a Senate committee in September that there were no manipulated wait times, remains in his job. Officials said that 1,100 employees across the department were terminated in 2014, but that those terminations were not directly related to actions taken as a result of the scandal.

“Not a single V.A. senior executive has been fired for wait-time manipulation,” Representative Jeff Miller, Republican of Florida and chairman of the House Veterans Affairs Committee, said in a statement this week ahead of the president’s visit to Phoenix. “What’s more, efforts to hold employees accountable in Phoenix have been repeatedly botched.”

Revelations about widespread problems at the hospitals started in Phoenix with the reports that 40 veterans had died while they were stuck on waiting lists to see doctors. The department’s inspector general later said that at least 1,700 veterans in Phoenix were “at risk of being forgotten or lost” in the hospital’s convoluted scheduling process.

All the while, the report said, the hospital falsely reported waiting times that suggested delays were minimal.

Other inquiries documented problems far beyond Phoenix. Rob Nabors, a former deputy chief of staff for Mr. Obama who was sent to work with the department, wrote last summer that a “corrosive culture has led to personnel problems across the department that are seriously impacting morale and, by extension, the timelines of health care.”