Comprehensive Tuberculosis Elimination Act of 2006 - Amends the Public Health Service Act to: (1) establish a national program for the elimination of tuberculosis and expand tuberculosis research and development activities and demonstration projects; (2) expand the duties and membership of the Advisory Council for the Elimination of Tuberculosis and require the Council to develop and implement a national plan to eliminate tuberculosis in the United States; (3) require the Secretary of Health and Human Services and the Federal Tuberculosis Task Force to develop new tools for the elimination of tuberculosis, including drugs, diagnostics, and vaccines; (4) require the Director of the National Heart, Lung, and Blood Institute of the National Institutes of Health (NIH) to expand, intensify, and coordinate NIH tuberculosis research, to make awards to faculties of medical and osteopathic schools to develop curricula for tuberculosis prevention, management, and control, and to make awards to support career development of clinically trained professionals committed to pulmonary infection research; (5) require the National Institute of Allergy and Infectious Diseases at NIH to work to develop a tuberculosis vaccine; (6) require the John E. Fogarty International Center for Advanced Study in the Health Sciences to carry out an international training program regarding tuberculosis; and (7) require the Secretary to ensure that a portion of funds appropriated to repay education loans of qualified health professionals, researchers from disadvantaged backgrounds, and clinical researchers is reserved for contracts with individuals who research tuberculosis.