Hazardous waste and innovation management systems in Latvia being on the incipience of development are full of contradictions and incompleteness despite of the fact that the both directly influence well-being of the state. Ecological damage reflecting on the natural and labour force presents particular threats to ecomonical position either immediately or over an extended period of time. Taking into account the threat of deficit of natural resources, the ecological situation which is greatly affected by hazardous waste, as the main determinant of national walfere, as well as taking into account the present conditon of waste management system, the one of the priorities of the National Innovation System in Latvia should be the innovation management of in the sphere of waste management. The most important aspect of the innovation implementation in hazardous waste managenent system is appreciation of efficiency. The investment in innovation of HWMS will lead to direct and indirect quantifiable and non-quantifiable economic benefits. So, the estimation of efficiency is inconvenient. In order to appreciate economic benefits we should measure not only economical, but also ecological efficiency what is the complex indicator.