Abstract-Hospital Information System (HIS) is important to healthcare sector especially in public hospitals as they need to serve the public with high-quality healthcare treatments. HIS helps to improve patients care services. Thus, the Malaysian Government has introduced three (3) categories of HIS namely Total Hospital Information System (THIS), Intermediate Hospital Information System (IHIS), and Basic Hospital Information System (BHIS) among Malaysian public hospitals. However, only 15.2% of the Malaysian public hospitals are implementing the system. Moreover, there is limited number of empirical studies on HIS implementation in Malaysia. Thus, this paper aims to investigate issues and challenges in HIS implementation for each category of HIS by using in-depth interviews. Nine participants were involved in the interviews. The interview data were transcribed verbatim and analysed based on Content and Thematic Analysis using NVivo software. The results showed that different category of HIS faced different issues and challenges.Index Terms-Basic hospital information system, hospital information system, intermediate hospital information system, total hospital information system.