Malaysian ports use the following regulations such as OSHA (Occupational, safety & Health Act) and EQA (Environmental Quality Act) to regulate health safety and the environment. However, the OSHA regulations do not cover safety on board ships while in port. Hence the ports use the Port Workers Safety rules under the Malaysian Merchant Shipping Ordinance (MSO).

When an accident or incident occurs within the port, if it involves safety of port staff, officers from the Department of Health and Safety (DOSH) will conduct the inquiry. However, if it occurs on board the vessel, then the Marine Department of Malaysia will conduct the inquiry. When an accident involves the environment, the Department of Science, Technology and Environment will conduct the investigation.

The Port Authority generally does conduct its own inquiry but with regard to penalties and punishment, the respective government departments will make the final decision.

With regard to port security, the Malaysian ports have already appointed their respective Port Facility Security Officers (PFSO). Port Facility Security Assessments (PFSA) are being conducted by the Marine Department of Malaysia and once that has been completed the Port Security Plan (PFSP) will be drawn up. Security Officers from the ports have already attended courses on the ISPS Code and its implications on port security which were conducted by the Marine Department who are the Designated Authority.

Two ports in Malaysia have been identified and included in the American Container Security Iniative (CSI) They are the port of Port Klang and Pelabuhan Tanjung Pelepas (PTP). These ports have been provided with scanners to screen containers entering the port and the customs will be using these to assist the U.S. Customs to screen containers bound for the United States. The CSI will be fully implemented in these ports by the 1st quarter of 2004.