Shipyard industry is one of the growing industry in Malaysia. There is still a lot of room for improvement with regards to the safety aspects within the industry. This study presents the finding of a survey on the safety management in shipyard operation of class C and D in Peninsular Malaysia registered with Ministry of Finance Malaysia. Shipyard operation is considered a hazardous job. Most of the cases were due to fall from height, fire and explosion. Similar accidents happened in South Korea, where 8 fatalities and 31 injuries were reported in January to August 2017. The accidents were due to crane collapsed and explosion during welding works inside a hull of a Liquefied Petroleum Gas (LPG) carrier. This paper aims to study the Health, Safety and Environment Management System (HSEMS) of shipyard operations in Malaysia particularly in Class C and Class D shipyard. This study was conducted using a survey method following the Glenn D's equation. The survey was targeted at the people who are involved in the industry including the staffs of clients, consultants and contractors. The findings of this study show that almost all the shipyards of Class C and D have HSEMS in placed but some are incomplete. Accidents still happen in the Malaysian shipyard industry from time to time. The gaps in the HSEMS that lead to the accident are highlighted in this paper. Nearly 10 of Class C and D shipyards do not have clear HSE Policy and this one of possible causes of accidents due to low priority given to HSE matters in this particular Class C and D shipyard. © The Authors, published by EDP Sciences, 2018.