Objective. To show that the administrative regime of specialized hospitals has some influence on the administrative processes to operate the Mexican Fund for Catastrophic Expenditures in Health (FPGC, in Spanish), for providing health care to breast cancer, cervical cancer and child leukemia. Materials and methods. The variable for estimating administrative efficiency was the time estimated from case notification to reimbursement. For its estimation, semistructured interviews were applied to key actors involved in management of cancer care financed by FPGC. Additionally, a group of experts was organized to make recommendations for improving processes. Results. Specialized hospitals with a decentralized scheme showed less time to solve the administrative process in comparison with the model on the hospitals dependent on State Health Services, where timing and intermediation levels were higher. Conclusions. Decentralized hospitals administrative scheme for specialized care is more efficient, because they tend to be more autonomous.