This study aimed to reflect the efficiency of hospitals under the Ministry of Health (MoH) before and after the implementation of Public Hospital Associations (PHAs). This study covered 3years before (2010-2012) and 3years after (2013-2015) the implementation. The population of the study included 865 hospitals under the MoH providing health care services in 81 provinces. No sample was selected; all hospitals were included under the scope of study. The provinces were chosen as the decision-making unit. Changes in the efficiency values of hospitals were analyzed with the Malmquist Total Factor Efficiency Index. The results showed that, for the pre-PHAs period, 24 provinces in 2010, 27 provinces from 2010 to 2011, and 32 provinces from 2011 to 2012 were assessed as efficient. From 2012, the year of implementation, to 2013, the number of efficient provinces dropped to 16. However, 20 provinces were subsequently found to be efficient from 2013 to 2014, and 26 from 2014 to 2015. The efficiency scores average of all provinces were found to be 0.89, 0.92, 0.92, 0.82, 0.88, and 0.90, respectively. Further, the efficiency score average of the 3years before PHAs (0.91 +/- 0.09) was significantly higher than the score obtained 3years after PHAs (0.86 +/- 0.11; p<0.05). In consideration of such finding, the PHAs established at the provinces were identified as hampering increased efficiency.