The strategic location of Malaysia along the world's busiest trade waterways underscores the need to cope ballast water issues for both domestic and international shipping. The adoption of Ballast Water Management Convention 2004 (BWMC) by the International Maritime Organization is suitable for management plans intended to prevent the introduction of invasive species through ballast water discharge. Malaysia has ratified the BWMC in September 2010 and the Convention has come into force in September 2017. However up to now, the BWMC has not been fully implemented by Malaysia for ships operating in its waters. This paper analyse the headway in implementing the provisions of the BWMC in Malaysia as well as the issues and challenges encountered for the implementation. The paper concludes that Malaysian government should promulgate laws and policies to clearly communicate on ballast water issues to the shipping industry communities.