OBJECTIVES: To reveal the main causes of non-compliance for technology incorporation requests into the Brazilian Public Health System (SUS) for the period of 2012 and 2013. METHODS: This was a descriptive cross-sectional study. The analysis was performed using the database of National Committee for Technology Incorporation (CONITEC) submitted applications for incorporation in the years 2012 and 2013. The CONITEC, which belongs to the Ministry of Health of Brazil, is responsible for the incorporation, exclusion or alteration of new medicines, procedures and products on the public health system. The presentation of economic evaluation by applicants (economic study and a budget impact analysis) is necessary to enable the analysis of the proposed requirements. RESULTS: Out of the 142 external (outside the Ministry of Health) requests submitted for analysis, 56 (39%) were non-compliant, 50 (89%) of them were due to problems in the economic evaluation. Out of the economically non-compliant, 16 (32%) presented problems in the economic study only  and 32 (64%) of them presented problems in both items. The main problems observed were not submitting an economic study, not submitting the economic model used in the study, and presenting an economic study using a different perspective than the one of SUS. CONCLUSIONS: The high percentage of non-compliance due to the economic evaluation points out the difficulty faced in completing these studies. It is important to invest in initiatives, human resources, training and spreading of economic evaluation knowledge which enables clarifying the required criteria for applying for an incorporation request.