(1) Background: Although Sri Lanka is a developing country and boasts of having a well-established healthcare system along with good healthcare indices, we are still lagging in certain aspects of healthcare. One such aspect is the deficiencies in guidelines and practices related to the handling of pharmaceutical waste. (2) Methods: This was a qualitative study performed using in-depth interviews with the help of a semi-structured questionnaire conducted among staff who are working at a ministry complex in Galle, Sri Lanka. Data analysis was performed using thematic analysis, (3) Results: There were 40 participants which included 29 (72.5%) females. Three main themes were identified, namely, (I) current knowledge, (II) perceptions, and (III) practices towards storage, disposal, and misuse of pharmaceutical waste. The death of the patient, forgetting, relieving symptoms, and adverse effects were some reasons for the accumulation of unused pharmaceuticals at home. Most of the participants did not believe that the reuse of unused medications can cause various health hazards. Moreover, all participants practiced unsafe methods such as flushing down toilets, pouring into a sink, burning, etc. (4) Conclusions: The incorrect practices and poor knowledge in the handling of pharmaceutical waste and less concern for the environment highlight the need for awareness programs to the general public and establishing proper medication waste management such drug take-back systems.