Modern scientific and technological changes have enabled online education as an integral part of the education system in the contemporary world. Although online learning system was influential in the pre-Covid 19 periods to a certain extent, it has become an inevitable part of the teaching and learning process of higher education sectors during the Covid-19 era. As the Covid-19 posed enormous challenges on the traditional higher education system, there was a desperate need globally for every government to incorporate online education into their higher education system. However, online education was not given much importance in the Sri Lankan higher education sector before the Covid-19. But, the closure of universities due to Covid-19 had prompted the government of Sri Lanka to promote the online mode of education as an alternative solution to continue higher education activity during a crisis. Thus, online education has presently become an essential component of Sri Lanka's higher education sector. Nevertheless, there are many obstacles and challenges confronting the higher education sectors, particularly in the universities of Sri Lanka to perpetuate online education successfully. Against this backdrop, this study attempts to give an insight into the impact of Covid-19 on the teaching and learning process of South Eastern University of Sri Lanka, and the challenges faced by the university in perpetuating online education system during the Covid-19. The findings of the study show that the university encountered several challenges in terms of online delivery, problems related to practical test via online mode, assessment, examination and supervision of the thesis. The study further highlights issues concerning online teaching and learning environment and a lack of online teaching and learning skills among staff and students that were considered critical to the smooth functioning of teaching and learning process of the South Eastern University of Sri Lanka during the Covid-19 pandemic. The study argues that the university should focus on a hybrid education system to address the issues of online mode of education confronted by staff and students to make the teaching and learning process more effective.