He held this post until 1971, earning the Distinguished Public Service Award from both the navy and the Department of Defense during his tenure. Bowsher returned to Arthur Anderson & Co., remaining until 1981, when President Reagan appointed him to a 15-year term as comptroller general of the United States General Accounting Office (GAO).
One of the longest sitting comptroller generals in the history of the United States, he was credited with increasing the responsibilities and influence of the GAO. Bowsher received honorary doctorates of public service from St. Joseph University and George Washington University and honorary doctorates of science from the University of Illinois–Chicago and Bryant University. He has been a member of the advisory committee of the Financial Accounting Standards Board, the American Institute of Certified Public Accountants, and the National Academy of Public Administration.