Abstract Background Research on information systems for mental health in low and middle income countries (LMICs) is scarce. As a result, there is a lack of reliable information on mental health service needs, treatment coverage and the quality of services provided. Methods With the aim of informing the development and implementation of a mental health information sub-system that includes reliable and measurable indicators on mental health within the Health Management Information Systems (HMIS), a cross-country situation analysis of HMIS was conducted in six LMICs (Ethiopia, India, Nepal, Nigeria, South Africa and Uganda), participating in the ‘Emerging mental health systems in low and middle income countries’ (Emerald) research programme. A situation analysis tool was developed to obtain and chart information from documents in the public domain. In circumstances when information was inadequate, key government officials were contacted to verify the data collected. In this paper we compare the baseline policy context, human resources situation as well as the processes and mechanisms of collecting, verifying, reporting and disseminating mental health related HMIS data. Results The findings suggest that countries face substantial policy, human resource and health governance challenges for mental health HMIS, many of which are common across sites. In particular, the specific policies and plans for the governance and implementation of mental health data collection, reporting and dissemination are absent. Across sites there is inadequate infrastructure, few HMIS experts, and inadequate technical support and supervision to junior staff, particularly in the area of mental health. Nonetheless there are also strengths in existing HMIS where a few mental health morbidity, mortality, and system level indicators are collected and reported. Conclusions Our study indicates the need for greater technical and resources input to strengthen routine HMIS and develop standardized HMIS indicators for mental health, focusing in particular on indicators of coverage and quality to facilitate the implementation of the WHO mental health action plan 2013–2020.