Innovation is highly critical for every company, especially for technology-based organizations looking to sustain their competitive advantage. However, this is not an easy task. Regardless of the size of the enterprise, market and location, all organizations face numerous challenges. Even though huge barriers to innovation exist in different countries, firm- and industry-specific challenges can be distinguished. This paper examines innovation strategies and obstacles to innovation in research and technology organizations (RTO) of Turkey. From the most important to the least, nine different challenges are ranked according the results of this survey. The findings reveal that to take the lead in innovation, financial constraint is the biggest challenge, which is consistent with the related literature. It ranked number one in this study. Beyond that, based on a sample of 40 RTOs, regional challenges such as underdeveloped regional innovation ecosystem plays a significant role in hampering innovation. Most of the organizations (55%) embrace an incremental approach to innovation, while only few pursue radical shifts. About 40% of the RTOs focus on product innovation, and 27.5% of them concentrate on technological innovation, while a very limited number aim for operational excellence and customer engagement as the focus of their strategic innovation efforts.