The aim of this study is to explore teachers’ perceptions and practices of instilling critical thinking skills in reading instruction, to enhance students’ reading comprehension. It also identifies perceived challenges that hinder the practice of critical thinking skills in reading classes. Methodology. The research was carried out at Hawassa University in Ethiopia, using a descriptive survey design and an explanatory mixed-methods approach to collecting data. Forty out of a total of fifty-two English educators and three reading teachers participated in this study. The questions were randomly selected. Texts used in quizzes, mid-term exams and final exams were chosen, to evaluate the texts in which teachers integrated critical thinking skills into classroom reading activities and assessments. Quantitative data was gathered through questionnaires, while qualitative data was obtained through document analysis. Statistical analysis was conducted using Statistical Package for the Social Sciences (SPSS), version 24, and content analysis was used for the qualitative data. Results. The survey results revealed that teachers had a moderate level of perception with regard to integrating critical thinking skills (m=3.59) and identified student-related challenges (m= 3.76) as significant obstacles to the practice of critical thinking skills. The results of document analysis indicated that the practice of critical thinking skills was infrequent. It can be concluded that teachers' conceptual perception at moderate level was not sufficient to incorporate critical thinking skills into reading instruction in order to enhance students' reading comprehension. Therefore, it is imperative to train teachers in the integration of critical thinking skills in an interactive reading curriculum to motivate and engage students and help them comprehend reading skills in greater depth. Further research is recommended to explore the impact of teachers' perceptions of critical thinking skills on students' reading comprehension.