Background: The results of international studies have concluded the low level of science literacy in natural science subjects of Slovak students. These studies also showed that this state can be positively influenced by various innovations, which are implemented into the teaching process of above-mentioned subjects. Purpose: The aim of this study is to identify existing problems and try to search for possible reasons of scientific literacy declination. We focused our attention toward the learning process, its elements and teacher-student interaction in this process. In our opinion, it should be possible to find some approaches on how to improve the results of the learning process and thus science literacy in the next PISA evaluation. Sample: Our research included 62 high school teachers from Slovakia, who do teach Biology, Chemistry, and Physics. Design and methods: The research was documented in a non-standardized questionnaire where the teachers were asked closed questions using a Likert response scale. The responses were evaluated by descriptive statistics using tables and graphs. Results: The research presented in this paper has revealed certain issues problems in contemporary education, leading to lower science literacy of Slovak students. Research has also investigated whether teachers have sufficient knowledge and experiences with the implementation of Problem-based learning (PBL) elements in their own teaching. It was observed that students have a reasonably good content knowledge, but an insufficient procedural and epistemic knowledge therefore they are unable to utilize them in problem-solving activities. Conclusions: Teachers were recommended to focus their pedagogical attention on the method of obtaining knowledge and the understanding problem solving in the wider context (qualitative knowledge, science understanding, scientific explanation of phenomena with its proper interpretation).