The main aim of the present study is to determine the influence of a Jigsaw method based on cooperative learning and a confirmatory laboratory method on prospective science teachers' achievements of physics in science teaching laboratory practice courses. The sample of this study consisted of 33 female and 15 male third-grade prospective science teachers (6th term) who attended science teaching laboratory practices course in the 2014-2015 academic year. In the research, science teaching laboratory practices course was carried out in accordance with a Jigsaw method based on cooperative learning in an experimental group and a confirmatory laboratory method in a control group. Following the treatment, Science Laboratory Physic Achievement Test (SLPAT) was administered as the post-test. The data obtained with the instruments were evaluated using descriptive statistics, independent samples t-test, and ANCOVA. The results indicated that the student teachers had higher levels of achievement in physics topics which were taught through the Jigsaw method based on cooperative learning than through a confirmatory laboratory method. In addition, according to the SLPAT results, students' high levels of misunderstanding revealed that there were problems in the teaching process of physics concepts. It was determined that the student teachers in the research groups had conceptual misunderstandings about sound, electricity, magnetism, light and optics issues. Based on the applications performed in this study, the original Jigsaw was adapted to science laboratory applications as an alternative to the existing Jigsaw techniques in the literature. With similar efforts, the experiences of prospective science teachers can be enhanced for implementing modern teaching methods in their respective areas in the pre-service period. Thus, the provision of professional development of the pre-service science teachers can be supported.