MSOs run the risk of offering poor services because the organizations, like any other business, attempt to perform at low output in a bid to lower operational costs. Therefore, the Service Level Agreement should govern them to ensure effective accountability in service delivery.
Creation of MSOs requires significant time investment due to the high amount of research that goes into their integration process in an institution's system. The organization should invest time in staff training, management restructuring, data sharing and facility transfer for facility transfers such as database management. This may also create disruptions in the facility's functioning during these periods.
MSOs may run into compatibility issues with institutions during the feasibility study and product development stages. An institution with a complex structure makes it difficult for the MSO to make products for it. This also includes conflicts resulting from the lack of suitability between the products availed by the MSO and the services offered by the institutions.
High costs resulting from setup and integration of MSO products into the system is one of the factors that discourage medical institutions or groups of doctors from joining such organizations. For example, in a database management service, the MSO requires that the data and the necessary equipment be moved to their base and that the client also install the necessary infrastructure to facilitate access from the institution. Since the MSO passes the cost to the institution, the whole process can be costly.