Within the last decade, Thailand has emerged as a South East Asian ‘innovation achiever’, partly due to its aggressive interest in developing its national innovation system (NIS) through a notorious increase in research and development (R&D) investment. However, the evaluation of the productivity of such domestic policies has been found unfit to the conditions of this emerging ecosystem. In particular, the assessment of interactions, amongst industry, academic, and government sectors, as an outcome of innovation promotion efforts is reported as a remaining challenge. Previous studies have compared the value of the inputs versus R&D outcomes & innovation activities and argued that certain effects of R&D collaboration hold a different worth depending on the NIS’ context. This study proposes a systematic method to examine which factors of collaboration affect firms on R&D productivity and how these reflect on the industrial sectors’ dynamics. Our focus is on Thailand, as an exemplary case of a developing, upper middle-income country, trying to ‘catch-up’ by enhancing national capacity. The proposed study contributes to the innovation management field as a differentiated approach pursuing a tuned fit to the challenging conditions of firms and policy-makers in emerging nations. The results explore not only direct proxies, such as the number of inventions, patent applications, and granted patents, but also illustrate, through an analytical model, the determinant factors that influence collaboration amongst firms (industry sector), with the academic and public sectors. Our study allows the assessment of innovation outcomes through the proportion of R&D expenditure from government and industry sectors, and the firm’s total sales. The model is tested empirically through a dataset collected directly from the national innovation status survey, performed on firms representing 44 industry sectors in Thailand, from 2011 to 2016. The study features significant conclusions regarding the innovation-led collaboration of firms and stakeholders in the government and industry sectors, for most of the two-year time lag. Our research contributes to practical guidance to policy-makers and practitioners who may design more accurate public policy and innovation promotion strategies that accommodate the challenging conditions typical of developing countries. As an example, based on these results, developing countries which face weak absorptive technological capacity may use the analytical model to tailor short-term national innovation planning, and assess R&D collaboration amongst industry and government sector stakeholders rather than using other traditional innovation promotion output proxies.