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Background  Despite improvements in a number of health outcome indicators partly due to the National Health Insurance Scheme (NHIS), Ghana is unlikely to attain all its health-related millennium development goals before the end of 2015. Inefficient use of available limited resources has been cited as a contributory factor for this predicament. This study sought to explore efficiency levels of NHIS-accredited private and public health facilities; ascertain factors that account for differences in efficiency and determine the association between quality care and efficiency levels.    Methods  The study is a cross-sectional survey of NHIS-accredited primary health facilities (n = 64) in two regions in southern Ghana. Data Envelopment Analysis was used to estimate technical efficiency of sampled health facilities while Tobit regression was employed to predict factors associated with efficiency levels. Spearman correlation test was performed to determine the association between quality care and efficiency.    Results  Overall, 20 out of the 64 health facilities (31 %) were optimally efficient relative to their peers. Out of the 20 efficient facilities, 10 (50 %) were Public/government owned facilities; 8 (40 %) were Private-for-profit facilities and 2 (10 %) were Private-not-for-profit/Mission facilities. Mission (Coef. = 52.1; p = 0.000) and Public (Coef. = 42.9; p = 0.002) facilities located in the Western region (predominantly rural) had higher odds of attaining the 100 % technical efficiency benchmark than those located in the Greater Accra region (largely urban). No significant association was found between technical efficiency scores of health facilities and many technical quality care proxies, except in overall quality score per the NHIS accreditation data (Coef. = −0.3158; p &lt; 0.05) and  SafeCare Essentials  quality score on environmental safety for staff and patients (Coef. = −0.2764; p &lt; 0.05) where the association was negative.    Conclusions  The findings suggest some level of wastage of health resources in many healthcare facilities, especially those located in urban areas. The Ministry of Health and relevant stakeholders should undertake more effective need analysis to inform resource allocation, distribution and capacity building to promote efficient utilization of limited resources without compromising quality care standards.

Efficiency of private and public primary health facilities accredited by the National Health Insurance Authority in Ghana